// This file is part of PLINK 2.0, copyright (C) 2005-2025 Shaun Purcell,
// Christopher Chang.
//
// This program is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the Free
// Software Foundation, either version 3 of the License, or (at your option)
// any later version.
//
// This program is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
// FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
// more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.

#include "plink2_help.h"

#include <string.h>

#include "include/plink2_bits.h"
#include "plink2_cmdline.h"

#ifdef __cplusplus
namespace plink2 {
#endif

const char kCmdlineFormatStr[] = "\n  plink2 <input flag(s)...> [command flag(s)...] [other flag(s)...]\n  plink2 --help [flag name(s)...]\n\n";

PglErr DispHelp(const char* const* argvk, uint32_t param_ct) {
  // yes, this is overkill.  But it should be a good template for other
  // command-line programs to use.
  uint32_t param_ctl = BitCtToWordCt(param_ct);
  PglErr reterr = kPglRetSuccess;
  const char** new_argv = nullptr;
  HelpCtrl help_ctrl;
  uint32_t arg_uidx;
  uint32_t arg_idx;
  uint32_t net_unmatched_ct;
  int32_t col_num;
  int32_t leading_dashes;
  help_ctrl.iters_left = param_ct? 2 : 0;
  help_ctrl.param_ct = param_ct;
  help_ctrl.unmatched_ct = param_ct;
  help_ctrl.param_slens = nullptr;
  help_ctrl.all_match_arr = nullptr;
  help_ctrl.argv = nullptr;
  if (param_ct) {
    if (unlikely(pgl_malloc(param_ct * sizeof(int32_t), &help_ctrl.param_slens) ||
                 pgl_malloc(param_ctl * 3 * sizeof(intptr_t), &help_ctrl.all_match_arr))) {
      goto DispHelp_ret_NOMEM;
    }
    leading_dashes = 0;
    for (arg_uidx = 0; arg_uidx != param_ct; ++arg_uidx) {
      if (argvk[arg_uidx][0] == '-') {
        leading_dashes = 1;
        break;
      }
    }
    if (leading_dashes) {
      if (unlikely(pgl_malloc(param_ct * sizeof(intptr_t), &new_argv))) {
        goto DispHelp_ret_NOMEM;
      }
      for (arg_uidx = 0; arg_uidx != param_ct; ++arg_uidx) {
        if (argvk[arg_uidx][0] == '-') {
          if (argvk[arg_uidx][1] == '-') {
            new_argv[arg_uidx] = &(argvk[arg_uidx][2]);
          } else {
            new_argv[arg_uidx] = &(argvk[arg_uidx][1]);
          }
        } else {
          new_argv[arg_uidx] = argvk[arg_uidx];
        }
      }
      help_ctrl.argv = new_argv;
    } else {
      help_ctrl.argv = argvk;
    }
    for (arg_idx = 0; arg_idx != param_ct; ++arg_idx) {
      help_ctrl.param_slens[arg_idx] = strlen(help_ctrl.argv[arg_idx]);
    }
    ZeroWArr(param_ctl * 3, help_ctrl.all_match_arr);
    help_ctrl.prefix_match_arr = &(help_ctrl.all_match_arr[param_ctl]);
    help_ctrl.perfect_match_arr = &(help_ctrl.all_match_arr[param_ctl * 2]);
    help_ctrl.preprint_newline = 1;
  } else {
    help_ctrl.argv = nullptr;
    fputs(
"\nIn the command line flag definitions that follow,\n"
"  * <angle brackets> denote a required parameter, where the text between the\n"
"    angle brackets describes its nature.\n"
"  * ['square brackets + single-quotes'] denotes an optional modifier.  Use the\n"
"    EXACT text in the quotes.\n"
"  * [{bar|separated|braced|bracketed|values}] denotes a collection of mutually\n"
"    exclusive optional modifiers (again, the exact text must be used).  When\n"
"    there are no outer square brackets, one of the choices must be selected.\n"
"  * ['quoted_text='<description of value>] denotes an optional modifier that\n"
"    must begin with the quoted text, and be followed by a value with no\n"
"    whitespace in between.  '|' may also be used here to indicate mutually\n"
"    exclusive options.\n"
"  * [square brackets without quotes or braces] denote an optional parameter,\n"
"    where the text between the brackets describes its nature.\n"
"  * An ellipsis (...) indicates that you may enter multiple arguments of the\n"
"    specified type.\n"
"  * A \"column set descriptor\" is either\n"
"    1. a comma-separated sequence of column set names; this is interpreted as\n"
"       the full list of column sets to include.\n"
"    2. a comma-separated sequence of column set names, all preceded by '+' or\n"
"       '-'; this is interpreted as a list of changes to the default.\n"
, stdout);
    fputs(kCmdlineFormatStr, stdout);
    fputs(
"Most PLINK runs require exactly one main input fileset.  The following flags\n"
"are available for defining its form and location:\n\n"
, stdout);
  }
  do {
    // explicit gzipped .pvar/.bim support was tried, and then rejected since
    // decompression was too slow
    // Zstd should have the necessary x86 performance characteristics, though
    HelpPrint("pfile\0pgen\0pgi\0bfile\0bed\0", &help_ctrl, 1,
"  --pfile <prefix> ['vzs']  : Specify .pgen[ + .pgen.pgi] + .pvar[.zst] +\n"
"                              .psam prefix.\n"
"  --pgen <filename>         : Specify full name of .pgen/.bed file.\n"
"  --pgi <filename>          : Specify full name of .pgen.pgi file.\n"
               );
    HelpPrint("pfile\0pgen\0pvar\0psam\0bfile\0bed\0bim\0fam\0dosage\0", &help_ctrl, 1,
"  --pvar <filename>         : Specify full name of .pvar/.bim file.\n"
              );
    HelpPrint("pfile\0pgen\0pvar\0psam\0bfile\0bed\0bim\0fam\0import-dosage\0dosage\0vcf\0bcf\0", &help_ctrl, 1,
"  --psam <filename>         : Specify full name of .psam/.fam file.\n\n"
               );
    HelpPrint("bfile\0bpfile\0bed\0bim\0fam\0", &help_ctrl, 1,
"  --bfile  <prefix> ['vzs'] : Specify .bed + .bim[.zst] + .fam prefix.\n"
"  --bpfile <prefix> ['vzs'] : Specify .pgen + .bim[.zst] + .fam prefix.\n\n"
               );
    HelpPrint("vcf\0bcf\0keep-autoconv\0", &help_ctrl, 1,
"  --keep-autoconv ['vzs']   : When importing non-PLINK-binary data, don't\n"
"                              delete autogenerated fileset at end of run.\n\n"
               );
    HelpPrint("bfile\0fam\0no-fid\0no-parents\0no-sex\0", &help_ctrl, 1,
"  --no-fid           : .fam file does not contain column 1 (family ID).\n"
"  --no-parents       : .fam file does not contain columns 3-4 (parents).\n"
"  --no-sex           : .fam file does not contain column 5 (sex).\n\n"
               );
    // probable todo: dosage=AD mode.
    HelpPrint("vcf\0bcf\0psam\0fam\0", &help_ctrl, 1,
"  --vcf <filename> ['dosage='<field>]\n"
"  --bcf <filename> ['dosage='<field>] :\n"
"    Specify full name of .vcf{|.gz|.zst} or BCF2 file to import.\n"
"    * These can be used with --psam/--fam.\n"
"    * By default, dosage information is not imported.  To import the GP field\n"
"      (must be VCFv4.3-style 0..1, one probability per possible genotype), add\n"
"      'dosage=GP' (or 'dosage=GP-force', see below).  To import Minimac3-style\n"
"      DS+HDS phased dosage, add 'dosage=HDS'.  'dosage=DS' (or anything else\n"
"      for now) causes the named field to be interpreted as a Minimac3-style\n"
"      dosage.\n"
"      Note that, in the dosage=GP case, PLINK 2 collapses the probabilities\n"
"      down to dosages; you cannot use PLINK 2 to losslessly convert VCF\n"
"      FORMAT/GP data to e.g. BGEN format.  To make this more obvious, PLINK 2\n"
"      now errors out when dosage=GP is used on a file with a FORMAT/DS header\n"
"      line and --import-dosage-certainty wasn't specified, since dosage=DS\n"
"      extracts the same information more quickly in this situation.  You can\n"
"      suppress this error with 'dosage=GP-force'.\n"
"      In all of these cases, hardcalls are regenerated from scratch from the\n"
"      dosages.  As a consequence, variants with no GT field can now be\n"
"      imported; they will be assumed to contain only diploid calls when HDS is\n"
"      also absent.\n\n"
              );
    HelpPrint("data\0gen\0bgen\0sample\0haps\0legend\0", &help_ctrl, 1,
"  --data <filename prefix> <REF/ALT mode> ['gzs']\n"
"  --bgen <filename> <REF/ALT mode> ['snpid-chr']\n"
"  --gen <filename> <REF/ALT mode>\n"
"  --sample <filename> :\n"
"    Specify an Oxford-format dataset to import.  --data specifies a .gen[.zst]\n"
"    + .sample pair, while --bgen specifies a BGEN v1.1+ file.\n"
"    * If a BGEN v1.2+ file contains sample IDs, it may be imported without a\n"
"      companion .sample file.\n"
"    * With 'snpid-chr', chromosome codes are read from the 'SNP ID' field\n"
"      instead of the usual chromosome field.\n"
"    * The following REF/ALT modes are supported:\n"
"      'ref-first': The first allele for each variant is REF.\n"
"      'ref-last': The last allele for each variant is REF.\n"
"      'ref-unknown': The last allele for each variant is treated as\n"
"                     provisional-REF.\n\n"
               );
    // todo: make 'per' prefix modifiable
    HelpPrint("haps\0legend\0", &help_ctrl, 1,
"  --haps <filename> [{ref-first | ref-last}]\n"
"  --legend <filename> <chr code> :\n"
"    Specify .haps [+ .legend] file(s) to import.\n"
"    * When --legend is specified, it's assumed that the --haps file doesn't\n"
"      contain header columns.\n"
"    * On chrX, the second male column may contain dummy '-' entries.  (However,\n"
"      PLINK 2 currently cannot handle omitted male columns.)\n"
"    * If not used with --sample, new sample IDs are of the form 'per#/per#'.\n\n"
               );
    HelpPrint("eigfile\0eigtfile\0eiggeno\0eigtgeno\0eigind\0eigsnp\0", &help_ctrl, 1,
"  --eigfile <filename prefix> ['nohash']\n"
"  --eiggeno <filename> ['nohash']\n"
"  --eigind <filename>\n"
"  --eigsnp <filename>\n"
"    Specify a .geno + .ind + .snp PACKEDANCESTRYMAP or TGENO dataset to import.\n"
"    * By default, this errors out when the sample-ID or variant-ID hash stored\n"
"      in the genotype file doesn't match the value computed from the .ind or\n"
"      .snp file.  Use the 'nohash' modifier to disable this behavior.\n"
"    * You can specify individual filenames with --eiggeno/--eigind/--eigsnp.\n\n"
              );
    HelpPrint("pedmap\0ped\0map\0file\0", &help_ctrl, 0,
"  --pedmap <prefix>  : Specify .ped + .map filename prefix.\n"
"  --ped <filename>   : Specify full name of .ped file.\n"
              );
    HelpPrint("pedmap\0map\0import-dosage\0dosage\0file\0", &help_ctrl, 1,
"  --map <filename>   : Specify full name of .map file.\n\n"
               );
    HelpPrint("tfile\0tped\0tfam\0", &help_ctrl, 1,
"  --tfile <prefix>   : Specify .tped + .tfam filename prefix.\n"
"  --tped <filename>  : Specify full name of .tped file.\n"
"  --tfam <filename>  : Specify full name of .tfam file.\n\n"
              );
    HelpPrint("import-dosage\0dosage\0map\0", &help_ctrl, 1,
"  --import-dosage <allele dosage file> ['noheader'] ['id-delim='<char>]\n"
"                  ['skip0='<i>] ['skip1='<j>] ['skip2='<k>] ['dose1']\n"
"                  ['format='<m>] [{ref-first | ref-last}]\n"
"                  ['single-chr='<code>] ['chr-col-num='<#>]\n"
"                  ['pos-col-num='<#>] :\n"
"    Specify PLINK 1.x-style dosage file to import.\n"
"    * You must also specify a companion .psam/.fam file.\n"
"    * By default, PLINK assumes that the file contains a header line, which has\n"
"      'SNP' in (1-based) column i+1, 'A1' in column i+j+2, 'A2' in column\n"
"      i+j+3, and sample FID/IIDs starting from column i+j+k+4.  (i/j/k are\n"
"      normally zero, but can be changed with 'skip0', 'skip1', and 'skip2'\n"
"      respectively.  FID/IID are normally assumed to be separate tokens, but if\n"
"      they're merged into a single token you can specify the delimiter with\n"
"      'id-delim='.)  If such a header line is not present, use the 'noheader'\n"
"      modifier; samples will then be assumed to appear in the same order as\n"
"      they do in the .psam/.fam file.\n"
"    * You may specify a companion .map file.  If you do not,\n"
"      * 'single-chr=' can be used to specify that all variants are on the named\n"
"        chromosome.  Otherwise, you can use 'chr-col-num=' to read chromosome\n"
"        codes from the given (1-based) column number.\n"
"      * 'pos-col-num=' causes bp coordinates to be read from the given column\n"
"        number.\n"
"    * The 'format=' modifier lets you specify the number of values used to\n"
"      represent each dosage.  'format=1' normally indicates a single 0..2 A1\n"
"      expected count; 'dose1' modifies this to a 0..1 frequency.  'format=2'\n"
"      indicates a 0..1 homozygous A1 likelihood followed by a 0..1 het\n"
"      likelihood.  'format=3' indicates 0..1 hom A1, 0..1 het, 0..1 hom A2.\n"
"      'format=infer' (the default) infers the format from the number of columns\n"
"      in the first nonheader line.\n\n"
               );
    // todo: triallelic rate
    HelpPrint("dummy\0", &help_ctrl, 1,
"  --dummy <sample ct> <SNP ct> [missing dosage freq(s)] [missing pheno freq]\n"
"          [{acgt | 1234 | 12}] ['pheno-ct='<count>] ['scalar-pheno']\n"
"          ['phase-freq='<rate>] ['dosage-freq='<rate>]\n"
"    This generates a fake input dataset with the specified number of samples\n"
"    and SNPs.\n"
"    * By default, the missing dosage frequency is zero.  This can be changed by\n"
"      providing a comma-separated list of possible frequencies (one frequency\n"
"      in the list is selected for each variant).\n"
"    * By default, the missing phenotype frequency is zero.  This can be changed\n"
"      by providing both a dosage-frequency and a 4th numeric argument; the 4th\n"
"      argument is then interpreted as the missing phenotype frequency.\n"
"    * By default, allele codes are As and Bs; this can be changed with the\n"
"      'acgt', '1234', or '12' modifier.\n"
"    * By default, one binary phenotype is generated.  'pheno-ct=' can be used\n"
"      to change the number of phenotypes, and 'scalar-pheno' causes these\n"
"      phenotypes to be normally distributed scalars.\n"
"    * By default, all genotypes/dosages are unphased.  To phase some of them,\n"
"      use 'phase-freq='.\n"
"    * By default, all dosages are in {0,1,2}.  To make some of them take on\n"
"      decimal values, use 'dosage-freq='.  (These dosages are affected by\n"
"      --hard-call-threshold and --dosage-erase-threshold.)\n\n"
               );
    HelpPrint("fa\0normalize\0ref-from-fa\0", &help_ctrl, 1,
"  --fa <filename>    : Specify full name of reference FASTA file.\n\n"
              );
    if (!param_ct) {
      fputs(
"Output files have names of the form 'plink2.<extension>' by default.  You can\n"
"change the 'plink2' prefix with\n\n"
, stdout);
    }
    HelpPrint("out\0", &help_ctrl, 1,
"  --out <prefix>     : Specify prefix for output files.\n\n"
              );
    if (!param_ct) {
      fputs(
"Most runs also require at least one of the following commands:\n\n"
, stdout);
    }
    HelpPrint("rm-dup\0list-duplicate-vars\0", &help_ctrl, 1,
"  --rm-dup [mode] ['list']\n"
"    Remove all but one instance of each duplicate-ID variant (ignoring the\n"
"    missing ID), and (with the 'list' modifier) write a list of duplicated IDs\n"
"    to <output prefix>.rmdup.list.\n"
"    The following modes of operation are supported:\n"
"    * 'error' (default) causes this to error out when there's a genotype data\n"
"      or other mismatch between the records.  A list of affected IDs is written\n"
"      to <output prefix>.rmdup.mismatch.\n"
"    * 'retain-mismatch' causes all instances of a duplicate-ID variant to be\n"
"      retained when there's a genotype data or variant info mismatch; otherwise\n"
"      one instance is kept.  The .rmdup.mismatch file is also written.\n"
"    * 'exclude-mismatch' removes all instances of duplicate-ID mismatched\n"
"      variants instead.\n"
"    * 'exclude-all' causes all instances of duplicate-ID variants to be\n"
"      removed, even when the actual records are identical.\n"
"    * 'force-first' causes only the first instance of duplicate-ID variants to\n"
"      be kept, under all circumstances.\n\n"
              );
    HelpPrint("make-pgen\0make-bpgen\0make-bed\0make-just-pvar\0make-just-psam\0make-pfile\0make-bpfile\0make-bfile\0", &help_ctrl, 1,
"  --make-pgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase']\n"
"              ['erase-dosage'] ['fill-missing-from-dosage'] ['writer-ver']\n"
"              ['pvar-cols='<col set desc>] ['psam-cols='<col set desc>]\n"
"  --make-bpgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase']\n"
"               ['erase-dosage'] ['fill-missing-from-dosage'] ['writer-ver']\n"
"  --make-bed ['vzs'] ['trim-alts']\n"
               /*
"  --make-pgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase']\n"
"              ['erase-dosage'] ['fill-missing-from-dosage'] ['writer-ver']\n"
"              ['multiallelics='<mode>]\n"
"              [{varid-split | varid-split-dup | varid-dup | varid-join}]\n"
"              ['pvar-cols='<col set desc>] ['psam-cols='<col set desc>]\n"
"  --make-bpgen ['vzs'] ['format='<code>] ['trim-alts'] ['erase-phase']\n"
"               ['erase-dosage'] ['fill-missing-from-dosage'] ['writer-ver']\n"
"               ['multiallelics='<mode>]\n"
"               [{varid-split | varid-split-dup | varid-dup | varid-join}]\n"
"  --make-bed ['vzs'] ['trim-alts'] ['multiallelics='<split mode>]\n"
               */
"    Create a new PLINK 2 binary fileset (--make-pgen = .pgen + .pvar[.zst] +\n"
"    .psam, --make-bpgen = .pgen + .bim[.zst] + .fam).\n"
"    * Unlike the automatic text-to-binary converters (which only heed\n"
"      chromosome filters), this supports all of PLINK's filtering flags.\n"
"    * The 'vzs' modifier causes the variant file (.pvar/.bim) to be\n"
"      Zstd-compressed.\n"
"    * The 'format' modifier requests an uncompressed fixed-variant-width .pgen\n"
"      file.  (These do not directly support multiallelic variants.)  The\n"
"      following format code is currently supported:\n"
"        2: just like .bed, except with an extended (12-byte instead of 3-byte)\n"
"           header containing variant/sample counts, and rotated genotype codes\n"
"           (00 = hom ref, 01 = het, 10 = hom alt, 11 = missing).\n"
               /*
"        3: unphased dosage data\n"
"        4: phased dosage data\n"
               */
"    * The 'trim-alts' modifier causes alternate alleles not present in the\n"
"      dataset after sample filtering to be removed.  (This occurs before any\n"
"      genotype/dosage erasure performed by --make-[b]pgen/--make-bed.)\n"
"    * The 'erase-phase' and 'erase-dosage' modifiers prevent phase and dosage\n"
"      information from being written to the new .pgen.\n"
"    * When a hardcall is missing but the corresponding dosage is present,\n"
"      'fill-missing-from-dosage' causes the (Euclidean-)nearest hardcall to be\n"
"      filled in, with ties broken in favor of the lower-index allele.\n"
"    * The 'writer-ver' modifier causes the output .pgen to include this\n"
"      program's version string.  Note that the resulting .pgen is not readable\n"
"      by plink2 builds from before May 2024.\n"
               /*
"    * The 'multiallelics=' modifier (alias: 'm=') specifies a join or split\n"
"      mode.  The following modes are currently supported:\n"
"      * '-': Split all multiallelic records.\n"
"      * '-snps': Split SNP-only multiallelic records.\n"
"      * '+'/'+both': Adjacent variants with identical CHROM/POS/REF are\n"
"                     classified as SNPs and non-SNPs; SNPs are joined into one\n"
"                     variant, and non-SNPs are joined into another.  This\n"
"                     errors out if any preexisting variant is mixed\n"
"                     SNP/non-SNP; split first in that case.  (Also see the\n"
"                     remark about symbolic ALT alleles below.)\n"
"      * '+snps': Similar to '+both', except only SNPs are joined.\n"
"      * '+any': All variants with identical CHROM/POS/REF and no symbolic ALT\n"
"                alleles are joined into a single multiallelic variant.\n"
"      Symbolic ALT alleles are joined separately.  Additional conditions apply\n"
"      to them, and PLINK 2 usually errors out when they aren't met.\n"
"      When splitting with 'varid-dup', the new variants keep the original\n"
"      variant ID.  Otherwise, new variant IDs are assigned as follows:\n"
"      1. If --set-all-var-ids was specified, that template is applied.\n"
"      2. Otherwise, if joining, and all source variant IDs are identical and\n"
"         nonmissing, that ID is used.\n"
"      3. Otherwise, if splitting with the 'varid-split' or 'varid-split-dup'\n"
"         modifier, the original variant ID is split on the ';' character when\n"
"         the number of ';'s is correct.  (When the post-split ID is the missing\n"
"         code, --set-missing-var-ids is applied to it.)  Similarly, if joining\n"
"         with the 'varid-join' modifier, the new variant ID is set to the\n"
"         original IDs joined with the ';' character when all original IDs are\n"
"         nonmissing and contain exactly one ';' per extra ALT allele.\n"
"      4. Otherwise, if splitting with 'varid-split-dup', the original ID is\n"
"         kept.\n"
"      5. Otherwise, if --set-missing-var-ids was specified, that template is\n"
"         applied.\n"
"      6. Otherwise, the variant ID is set to the missing code.\n"
"      When merging, the new variant gets the lowest QUAL and the union of the\n"
"      FILTER values.\n"
"      INFO splitting/merging is under development; for now, 'bcftools norm'\n"
"      (possibly on a single-sample file) can be used for this.\n"
"    * When the 'trim-alts', 'multiallelics=', and/or 'erase-...' modifier is\n"
"      present, --make-bed/--make-[b]pgen cannot be combined with other\n"
"      commands.  (They can be combined with other filters.)\n"
               */
"    * The first five columns of a .pvar file are always #CHROM/POS/ID/REF/ALT.\n"
"      Supported optional .pvar column sets are:\n"
"        xheader: All pre-#CHROM header lines (yeah, this is technically not a\n"
"                 column), except for possibly FILTER/INFO definitions when\n"
"                 those column(s) have been removed.  Without this, only the\n"
"                 #CHROM header line is kept.\n"
"        vcfheader: xheader, with additions to make it a valid VCF header.\n"
"        maybequal: QUAL.  Omitted if all remaining values are missing.\n"
"        qual: Force QUAL column to be written even when empty.\n"
"        maybefilter: FILTER.  Omitted if all remaining values are missing.\n"
"        filter: Force FILTER column to be written even when empty.\n"
"        maybeinfo: INFO.  Omitted if all remaining values are missing, or if\n"
"                   INFO/PR is the only subfield.\n"
"        info: Force INFO column to be written.\n"
"        maybecm: Centimorgan coordinate.  Omitted if all remaining values = 0.\n"
"        cm: Force CM column to be written even when empty.\n"
"      The default is xheader,maybequal,maybefilter,maybeinfo,maybecm.\n"
"    * Supported column sets for the .psam file are:\n"
"        maybefid: Family ID, '0' = missing.  Omitted if all values missing.\n"
"        fid: Force FID column to be written even when empty.\n"
"        maybesid: Source ID, '0' = missing.  Omitted if all values missing.\n"
"        sid: Force SID column to be written even when empty.\n"
"        maybeparents: Father and mother IIDs.  Omitted if all values missing.\n"
"        parents: Force PAT and MAT columns to be written even when empty.\n"
"        sex: '1' = male, '2' = female, 'NA' = missing.\n"
"        pheno1: First active phenotype.  If none, all column entries are set to\n"
"                the --output-missing-phenotype string.\n"
"        phenos: All active phenotypes, if any.  (Can be combined with pheno1 to\n"
"                force at least one phenotype column to be written.)\n"
"      The default is maybefid,maybesid,maybeparents,sex,phenos.\n\n"
              );
    HelpPrint("make-just-pvar\0make-just-psam\0make-just-bim\0make-just-fam\0write-cluster\n\0", &help_ctrl, 1,
"  --make-just-pvar ['zs'] ['cols='<column set descriptor>]\n"
"  --make-just-psam ['cols='<column set descriptor>]\n"
"  --make-just-bim ['zs']\n"
"  --make-just-fam\n"
"    Variants of --make-pgen/--make-bed which only write a new variant or sample\n"
"    file.  These don't always require an input genotype file.\n"
"    USE THESE CAUTIOUSLY.  It is very easy to desynchronize your binary\n"
"    genotype data and your sample/variant indexes if you use these commands\n"
"    improperly.  If you have any doubt, stick with --make-[b]pgen/--make-bed.\n\n"
              );
    HelpPrint("export\0recode\0", &help_ctrl, 1,
"  --export <output format(s)...> [{01 | 12}] ['bgz'] ['id-delim='<char>]\n"
"                                 ['id-paste='<col set descrip>] ['include-alt']\n"
"                                 ['omit-nonmale-y'] ['spaces']\n"
"                                 ['vcf-dosage='<field>] ['ref-first']\n"
"                                 ['bits='<#>] ['sample-v2']\n"
"                                 ['bgen-omit-sample-id-block']\n"
"    Create a new fileset with all filters applied.  The following output\n"
"    formats are supported:\n"
"    (actually, only A, AD, Av, bcf, bgen-1.x, eig, haps, hapslegend,\n"
"    ind-major-bed, oxford, ped, phylip, phylip-phased, tped, and vcf are\n"
"    implemented for now)\n"
"    * '23': 23andMe 4-column format.  This can only be used on a single\n"
"            sample's data (--keep may be handy), and does not support\n"
"            multicharacter allele codes.\n"
"    * 'A': Sample-major additive (0/1/2) coding, suitable for loading from R.\n"
"           If you need uncounted alleles to be named in the header line, add\n"
"           the 'include-alt' modifier.\n"
"    * 'AD': Sample-major additive (0/1/2) + dominant (het=1/hom=0) coding.\n"
"            Also supports 'include-alt'.\n"
"    * 'Av': Variant-major 0/1/2.\n"
"    * 'beagle': Unphased per-autosome .dat and .map files, readable by early\n"
"                BEAGLE versions.\n"
"    * 'beagle-nomap': Single .beagle.dat file.\n"
"    * 'bgen-1.x': Oxford-format .bgen + .sample.  For v1.2/v1.3, sample\n"
"                  identifiers are stored in the .bgen (with id-delim and\n"
"                  id-paste settings applied), and default precision is 16-bit\n"
"                  (use the 'bits' modifier to reduce this).\n"
"    * 'bimbam': Regular BIMBAM format.\n"
"    * 'bimbam-1chr': BIMBAM format, with a two-column .pos.txt file.  Does not\n"
"                     support multiple chromosomes.\n"
"    * 'eig', 'eigt': EIGENSOFT .geno + .ind + .snp format.  Does not support\n"
"                     multicharacter allele codes.\n"
"    * 'fastphase': Per-chromosome fastPHASE files, with\n"
"                   .chr-<chr #>.phase.inp filename extensions.\n"
"    * 'fastphase-1chr': Single .phase.inp file.  Does not support\n"
"                        multiple chromosomes.\n"
"    * 'haps', 'hapslegend': Oxford-format .haps + .sample[ + .legend].  All\n"
"                            data must be biallelic and phased.  When the 'bgz'\n"
"                            modifier is present, the .haps file is\n"
"                            block-gzipped.\n"
"    * 'HV': Per-chromosome Haploview files, with .chr-<chr #>{.ped,.info}\n"
"            filename extensions.\n"
"    * 'HV-1chr': Single Haploview .ped + .info file pair.  Does not support\n"
"                 multiple chromosomes.\n"
"    * 'ind-major-bed': PLINK 1 sample-major .bed (+ .bim + .fam).\n"
"    * 'lgen': PLINK 1 long-format (.lgen + .fam + .map), loadable with --lfile.\n"
"    * 'lgen-ref': .lgen + .fam + .map + .ref, loadable with --lfile +\n"
"                  --reference.\n"
"    * 'list': Single genotype-based list, up to 4 lines per variant.  To omit\n"
"              nonmale genotypes on the Y chromosome, add the 'omit-nonmale-y'\n"
"              modifier.\n"
"    * 'rlist': .rlist + .fam + .map fileset, where the .rlist file is a\n"
"                genotype-based list which omits the most common genotype for\n"
"                each variant.  Also supports 'omit-nonmale-y'.\n"
"    * 'oxford', 'oxford-v2': Oxford-format .gen + .sample.  When the 'bgz'\n"
"                             modifier is present, the .gen file is\n"
"                             block-gzipped.  'oxford' requests the original\n"
"                             .gen file format with 5 leading columns\n"
"                             (understood by older PLINK builds); 'oxford-v2'\n"
"                             requests the current 6-leading-column flavor.\n"
"    * 'ped', 'compound-genotypes': PLINK 1 sample-major (.ped + .map),\n"
"                                   loadable with --pedmap.\n"
"    * 'phylip': Relaxed PHYLIP format, IUPAC ambiguity codes used for hets.\n"
"    * 'phylip-phased': Relaxed PHYLIP format, but with two alignments per\n"
"                       sample.  Input must be fully phased.\n"
"    * 'structure': Structure-format.\n"
"    * 'tped': PLINK 1 variant-major (.tped + .tfam), loadable with --tfile.\n"
"    * 'vcf',     : VCF (default version 4.3).  If PAR1 and PAR2 are present,\n"
"      'vcf-4.2',   they are automatically merged with chrX, with proper\n"
"      'bcf',       handling of chromosome codes and male ploidy.\n"
"      'bcf-4.2'    When the 'bgz' modifier is present, the VCF file is\n"
"                   block-gzipped.  (This always happens with BCF output.)\n"
"                   The 'id-paste' modifier controls which .psam columns are\n"
"                   used to construct sample IDs (choices are maybefid, fid,\n"
"                   iid, maybesid, and sid; default is maybefid,iid,maybesid),\n"
"                   while the 'id-delim' modifier sets the character between the\n"
"                   ID pieces (default '_').\n"
"                   Genotypes are always exported.  If you want to export a\n"
"                   sites-only VCF instead, see --make-pgen/--make-just-pvar's\n"
"                   'vcfheader' column set.\n"
"                   Dosages are not exported unless the 'vcf-dosage=' modifier\n"
"                   is present.  The following six dosage export modes are\n"
"                   supported:\n"
"                   'GP': genotype posterior probabilities (v4.3 only).\n"
"                   'DS': Minimac3-style dosages, omitted for hardcalls.\n"
"                   'DS-force': Minimac3-style dosages, never omit.\n"
"                   'DS-only': Same as DS-force, except GT field is omitted.\n"
"                   'HDS': Minimac3-style phased dosages, omitted for hardcalls\n"
"                          and unphased calls.  Also includes 'DS' output.\n"
"                   'HDS-force': Always report DS and HDS.\n"
               // possible todo: pedigree output?
"    In addition,\n"
"    * The '12' modifier causes ref alleles to be coded as '1' and alt1 alleles\n"
"      to be coded as '2', while '01' maps ref -> 0 and alt1 -> 1.  Note that\n"
"      this is essentially the reverse of PLINK 1.x; the reversal was not\n"
"      properly documented before 7 Mar 2023.\n"
"    * The 'spaces' modifier makes the output space-delimited instead of\n"
"      tab-delimited, whenever both are permitted.\n"
"    * The 'used-sites' modifier causes a .used_sites.tsv file to be included\n"
"      with PHYLIP-format output.\n"
"    * For biallelic formats where it's unspecified whether the reference/major\n"
"      allele should appear first or second, --export defaults to second for\n"
"      compatibility with PLINK 1.9.  Use 'ref-first' to change this.\n"
"      (Note that this doesn't apply to the 'A', 'AD', and 'Av' formats; use\n"
"      --export-allele to control which alleles are counted there.)\n"
"    * 'sample-v2' exports .sample files according to the QCTOOLv2 rather than\n"
"      the original specification.  Only one ID column is exported ('id-paste'\n"
"      and 'id-delim' settings apply), parental IDs are exported if present, and\n"
"      category names are preserved rather than converted to positive integers.\n"
"    * 'bgen-omit-sample-id-block' causes the sample ID block to be omitted from\n"
"      exported bgen-1.2 and -1.3 files.\n\n"
              );
    // don't bother with case/control or cluster-stratification any more, since
    // user can loop through subgroups and then use Unix cut/paste

    // todo: add optional column for computed MAF (nothing here quite
    // corresponds to nonmajor_freqs when e.g. --maf-pseudocount is specified).
    HelpPrint("freq\0mach-r2-filter\0", &help_ctrl, 1,
"  --freq ['zs'] ['counts'] ['cols='<column set descriptor>] ['bins-only']\n"
"         ['refbins='<comma-separated bin boundaries> | 'refbins-file='<file>]\n"
"         ['alt1bins='<comma-separated bin boundaries> | 'alt1bins-file='<file>]\n"
"    Empirical allele frequency report.  By default, only founders are\n"
"    considered.  Dosages are taken into account (e.g. heterozygous haploid\n"
"    calls count as 0.5).\n"
"    Supported column sets are:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      (ID is always present, and positioned here.)\n"
"      ref: Reference allele.\n"
"      alt1: Alternate allele 1.\n"
"      alt: All alternate alleles, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present in\n"
"                    the main dataset, and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      reffreq: Reference allele frequency/dosage.\n"
"      alt1freq: Alt1 frequency/dosage.\n"
"      altfreq: Comma-separated frequencies/dosages for all alternate alleles.\n"
"      freq: Similar to altfreq, except ref is also included at the start.\n"
"      eq: Comma-separated <allele>=<freq> for all present alleles.  (If no\n"
"          alleles are present, the column contains a single '.'.)\n"
"      eqz: Same as eq, except zero-counts are included.\n"
"      alteq/alteqz: Same as eq/eqz, except reference allele is omitted.\n"
"      numeq: 0=<freq>,1=<freq>, etc.  Zero-counts are omitted.\n"
"      altnumeq: Same as numeq, except reference allele is omitted.\n"
"      machr2: Unphased MaCH imputation quality metric.\n"
"      minimac3r2: Phased Minimac3 imputation quality.\n"
"      nobs: Number of allele observations.\n"
"    The default is chrom,ref,alt,maybeprovref,altfreq,nobs.\n"
"    Additional .afreq.{ref,alt1}.bins (or .acount.{ref,alt1}.bins with\n"
"    'counts') file(s) are generated when 'refbins='/'refbins-file=' or\n"
"    'alt1bins='/'alt1bins-file=' is present; these report the total number of\n"
"    frequencies or counts in each left-closed, right-open interval.  (If you\n"
"    only want these histogram(s), and not the main report, add 'bins-only'.)\n\n"
              );
    // this can't really handle dosages, so we specify "hardcall"
    HelpPrint("geno-counts\0freq\0freqx\frqx\0", &help_ctrl, 1,
"  --geno-counts ['zs'] ['cols='<column set descriptor>]\n"
"    Variant-based hardcall genotype count report (considering both alleles\n"
"    simultaneously in the diploid case).  Nonfounders are now included; use\n"
"    --keep-founders if this is a problem.  Heterozygous haploid calls are\n"
"    treated as missing; mixed MT calls are not.\n"
"    Supported column sets are:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      (ID is always present, and positioned here.)\n"
"      ref: Reference allele.\n"
"      alt1: Alternate allele 1.\n"
"      alt: All alternate alleles, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present,\n"
"                    and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      homref: Homozygous-ref count.\n"
"      refalt1: Heterozygous ref-alt1 count.\n"
"      refalt: Comma-separated het ref-altx counts.\n"
"      homalt1: Homozygous-alt1 count.\n"
"      altxy: Comma-separated altx-alty counts, in (1/1)-(1/2)-(2/2)-(1/3)-...\n"
"             order.\n"
"      xy: Similar to altxy, except the reference allele is treated as alt0,\n"
"          and the sequence starts (0/0)-(0/1)-(1/1)-(0/2)-...\n"
"      hapref: Haploid-ref count.\n"
"      hapalt1: Haploid-alt1 count.\n"
"      hapalt: Comma-separated haploid-altx counts.\n"
"      hap: Similar to hapalts, except ref is also included at the start.\n"
"      numeq: 0/0=<hom ref ct>,0/1=<het ref-alt1>,1/1=<hom alt1>,...,0=<hap ref>\n"
"             etc.  Zero-counts are omitted.  (If all genotypes are missing, the\n"
"             column contains a single '.'.)\n"
"      missing: Number of missing genotypes.\n"
"      nobs: Number of (nonmissing) genotype observations.\n"
"    The default is chrom,ref,alt,maybeprovref,homref,refalt,altxy,hapref,\n"
"    hapalt,missing.\n\n"
              );
    // All weirdnesses in the default column-set are for the sake of minimizing
    // differences from the PSC section of bcftools stats -s.
    // There's no homsnp or homrefsnp column set since there's no good way to
    // define their behavior for multiallelic mixed SNP/non-SNP variants, and
    // --snps-only already exists.
    HelpPrint("sample-counts\0geno-counts\0", &help_ctrl, 1,
"  --sample-counts ['zs'] ['cols='<column set descriptor>]\n"
"    Sample-based hardcall genotype count report.\n"
"    * Unknown-sex samples are treated as female.\n"
"    * Heterozygous haploid calls (MT included) are treated as missing.\n"
"    * As with other PLINK 2 commands, SNPs that have not been left-normalized\n"
"      are counted as non-SNP non-symbolic.  (Use e.g. --normalize when that's a\n"
"      problem.)\n"
"    * Supported column sets are:\n"
"        maybefid: FID, if that column was present in the input.\n"
"        fid: Force FID column to be written even when absent in the input.\n"
"        (IID is always present, and positioned here.)\n"
"        maybesid: SID, if that column was present in the input.\n"
"        sid: Force SID column to be written even when absent in the input.\n"
"        sex: '1' = male, '2' = female, 'NA' = missing.\n"
"        hom: Homozygous genotype count.\n"
"        homref: Homozygous-ref genotype count.\n"
"        homalt: Homozygous-alt genotype count.\n"
"        homaltsnp: Homozygous-alt SNP count.\n"
"        het: Heterozygous genotype count.\n"
"        refalt: Heterozygous ref-altx genotype count.\n"
"        het2alt: Heterozygous altx-alty genotype count.\n"
"        hetsnp: Heterozygous SNP count.\n"
"        dipts: Diploid SNP transition count.\n"
"        ts: SNP transition count (excluding chrY for females).\n"
"        diptv: Diploid SNP transversion count.\n"
"        tv: SNP transversion count.\n"
"        dipnonsnpsymb: Diploid non-SNP, non-symbolic count.\n"
"        nonsnpsymb: Non-SNP, non-symbolic count.\n"
"        symbolic: Symbolic variant count.\n"
"        nonsnp: Non-SNP count.\n"
"        dipsingle: Number of singletons relative to this dataset, across just\n"
"                   diploid calls.  (Note that if the ALT allele in a chrX\n"
"                   biallelic variant appears in exactly one female and one\n"
"                   male, that counts as a singleton for just the female.)\n"
"        single: Number of singletons relative to this dataset.\n"
"        haprefwfemaley: Haploid-ref count, counting chrY for everyone.\n"
"        hapref: Haploid-ref count, excluding chrY for females.\n"
"        hapaltwfemaley: Haploid-alt count, counting chrY for everyone.\n"
"        hapalt: Haploid-alt count, excluding chrY for females.\n"
"        missingwfemaley: Missing call count, counting chrY for everyone.\n"
"        missing: Missing call count, excluding chrY for females.\n"
"      The default is maybefid,maybesid,homref,homaltsnp,hetsnp,dipts,diptv,\n"
"      dipnonsnpsymb,dipsingle,haprefwfemaley,hapaltwfemaley,missingwfemaley.\n"
"    * The 'hetsnp', 'dipts'/'ts'/'diptv'/'tv', 'dipnonsnpsymb'/'nonsnpsymb',\n"
"      'symbolic', and 'nonsnp' columns count each ALT allele in a heterozygous\n"
"      altx-alty call separately, since they can be of different subtypes.\n"
"      (I.e. if they are of the same subtype, the corresponding count is\n"
"      incremented by 2.)  As a consequence, these columns are unaffected by\n"
"      variant split/join.\n\n"
              );
    // todo: add cluster-stratification
    HelpPrint("missing\0", &help_ctrl, 1,
"  --missing ['zs'] [{sample-only | variant-only}]\n"
"            ['scols='<column set descriptor>] ['vcols='<column set descriptor>]\n"
"    Generate sample- and variant-based missing data reports (or just one report\n"
"    if 'sample-only'/'variant-only' is specified).\n"
"    Mixed MT hardcalls appear in the heterozygous haploid stats.\n"
"    Supported column sets in the sample-based report are:\n"
"      maybefid: FID, if that column was present in the input.\n"
"      fid: Force FID column to be written even when absent in the input.\n"
"      (IID is always present, and positioned here.)\n"
"      maybesid: SID, if that column was present in the input.\n"
"      sid: Force SID column to be written even when absent in the input.\n"
"      misspheno1: First active phenotype missing (Y/N)?  Always 'Y' if no\n"
"                  phenotypes are loaded.\n"
"      missphenos: A Y/N column for each loaded phenotype.  (Can be combined\n"
"                  with misspheno1 to force at least one such column.)\n"
"      nmissdosage: Number of missing dosages.\n"
"      nmiss: Number of missing hardcalls, not counting het haploids.\n"
"      nmisshh: Number of missing hardcalls, counting het haploids.\n"
"      hethap: Number of heterozygous haploid hardcalls.\n"
"      nobs: Denominator (male count on chrY, otherwise total sample count).\n"
"      fmissdosage: Missing dosage rate.\n"
"      fmiss: Missing hardcall rate, not counting het haploids.\n"
"      fmisshh: Missing hardcall rate, counting het haploids.\n"
"    The default is maybefid,maybesid,missphenos,nmiss,nobs,fmiss.\n"
"    Supported column sets in the variant-based report are:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      (ID is always present, and positioned here.)\n"
"      ref: Reference allele.\n"
"      alt1: Alternate allele 1.\n"
"      alt: All alternate alleles, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present,\n"
"                    and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      nmissdosage: Number of missing dosages.\n"
"      nmiss: Number of missing hardcalls, not counting het haploids.\n"
"      nmisshh: Number of missing hardcalls, counting het haploids.\n"
"      hethap: Number of heterozygous haploid calls.\n"
"      nobs: Number of potentially valid calls.\n"
"      fmissdosage: Missing dosage rate.\n"
"      fmiss: Missing hardcall rate, not counting het haploids.\n"
"      fmisshh: Missing hardcall rate, counting het haploids.\n"
"      fhethap: Heterozygous haploid rate.\n"
"    The default is chrom,maybeprovref,nmiss,nobs,fmiss.\n\n"
              );
    HelpPrint("hardy\0", &help_ctrl, 1,
"  --hardy ['zs'] ['midp'] ['log10'] ['redundant'] ['cols='<col set descriptor>]\n"
"    Hardy-Weinberg exact test p-value report(s).\n"
"    * By default, only founders are considered; change this with --nonfounders.\n"
"    * chrX is now omitted from the main <output prefix>.hardy report.  Instead,\n"
"      (if present) it gets its own <output prefix>.hardy.x report based on the\n"
"      method described in Graffelman J, Weir BS (2016) Hardy-Weinberg\n"
"      equilibrium and the X chromosome.\n"
"    * The 'log10' modifier causes p-values to be reported in -log10(p) form.\n"
"      Note that PLINK 2 accurately calculates and reports p-values smaller than\n"
"      DBL_MIN, but other software may not be able to read such values unless\n"
"      they are reported in -log10(p) form.\n"
"    * For variants with j alleles where j>2, j separate 'biallelic' tests are\n"
"      performed, each reported on its own line.  However, biallelic variants\n"
"      are normally reported on a single line, since the counts/frequencies\n"
"      would be mirror-images and the p-values would be the same.  You can add\n"
"      the 'redundant' modifier to force biallelic variant results to be\n"
"      reported on two lines for parsing convenience.\n"
"    * There is currently no special handling of case/control phenotypes.\n"
"    Supported column sets are:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      (ID is always present, and positioned here.)\n"
"      ref: Reference allele.\n"
"      alt1: Alternate allele 1.\n"
"      alt: All alternate alleles, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present,\n"
"                    and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      (A1 is always present, and positioned here.)\n"
"      ax: Non-A1 allele(s), comma-separated.\n"
"      gcounts: Hom-A1 count, total number of het-A1 calls, and total number of\n"
"               nonmissing calls with no copies of A1.  On chrX, these are\n"
"               followed by male A1 and male non-A1 counts.\n"
"      gcount1col: gcounts values in a single comma-separated column.\n"
"      hetfreq: Observed and expected het-A1 frequencies.\n"
"      sexaf: Female and male A1 observed allele frequencies (chrX only).\n"
"      femalep: Female-only p/midp-value (chrX only).\n"
"      p: Hardy-Weinberg equilibrium exact test p/midp-value (or -log10(p)).\n"
"    The default is chrom,maybeprovref,ax,gcounts,hetfreq,sexaf,p.\n\n"
               );
    HelpPrint("mendel\0", &help_ctrl, 1,
"  --mendel ['zs'] ['summaries-only'] ['cols='<column set descriptor>]\n"
"    Generate a Mendel error report.\n"
"    * chrY and chrM are no longer excluded from this analysis.\n"
"    * Heterozygous chrX male and chrY genotypes are treated as missing.\n"
"    * On chrM, when a child has a mixed hardcall, there is only a Mendel error\n"
"      if the mother has a nonmissing hardcall matching neither allele.\n"
"    * The 'summaries-only' modifier causes the .mendel[.zst] file (listing\n"
"      every single error) to be skipped.\n"
"    Supported column sets are:\n"
"      .mendel[.zst]:\n"
"        maybefid: FID, if that column was present in the input.\n"
"        fid: Force FID column to be written even when absent in the input.\n"
"        (KID with the kid's IID is always present, and positioned here.)\n"
"        maybesid: (Kid's) SID, if that column was present in the input.\n"
"        sid: Force SID column to be written even when absent in the input.\n"
"        chrom: Chromosome ID.\n"
"        pos: Base-pair coordinate.\n"
"        (ID with the variant ID is always present, and positioned here.)\n"
"        ref: Reference allele.\n"
"        alt: All alternate alleles, comma-separated.\n"
"        code: Numeric error code.\n"
"        error: Description of error.\n"
"      Specific to .imendel:\n"
"        trionum: 1-based trio/duo number.\n"
"        ni: Sample's Mendel error count (only considering trio/duo).\n"
"        nobsi: Number of variants considered.\n"
"        fraci: Sample's Mendel error rate (only considering trio/duo).\n"
"      Specific to .lmendel[.zst]:\n"
"        nl: Variant's Mendel error count.\n"
"        nobsl: Number of trios considered.\n"
"        fracl: Variant's Mendel error rate.\n"
"    The default is maybefid,maybesid,chrom,code,error,ni,nl.\n"
"    The maybefid/fid settings also apply to the .fmendel output file;\n"
"    maybefid/fid/maybesid/sid to the .imendel output file; and\n"
"    chrom/pos/ref/alt to the .lmendel[.zst] output file.\n\n"
              );
    HelpPrint("het\0", &help_ctrl, 1,
"  --het ['zs'] ['small-sample'] ['cols='<column set descriptor>]\n"
"    Inbreeding coefficient report.  Supports multiallelic variants.\n"
"    * This function requires decent MAF estimates.  If there are very few\n"
"      samples in your immediate fileset, --read-freq is practically mandatory\n"
"      since imputed MAFs are wildly inaccurate in that case.\n"
"    * It's usually best to perform this calculation on a variant set in\n"
"      approximate Hardy-Weinberg and linkage equilibrium.\n"
"    * By default, --het omits the n/(n-1) multiplier in Nei's expected\n"
"      homozygosity formula.  The 'small-sample' modifier causes it to be\n"
"      included, while forcing --het to use MAFs imputed from founders in the\n"
"      immediate dataset.\n"
"    Supported column sets are:\n"
"      maybefid: FID, if that column was present in the input.\n"
"      fid: Force FID column to be written even when absent in the input.\n"
"      (IID is always present, and positioned here.)\n"
"      maybesid: SID, if that column was present in the input.\n"
"      sid: Force SID column to be written even when absent in the input.\n"
"      hom: Observed and expected numbers of homozygous genotypes.\n"
"      het: Observed and expected numbers of heterozygous genotypes.\n"
"      nobs: Number of (nonmissing) genotype observations.\n"
"      f: Method-of-moments F coefficient estimate.\n"
"    The default is maybefid,maybesid,hom,nobs,f.\n\n"
              );
    HelpPrint("check-sex\0impute-sex\0update-sex\0sex-check\0", &help_ctrl, 1,
"  --check-sex ['max-female-xf='<x>] ['min-male-xf='<y>]\n"
"              ['max-female-ycount='<z>] ['min-male-ycount='<w>]\n"
"              ['max-female-yrate='<v>] ['min-male-yrate='<u>]\n"
"              ['cols='<column set descriptor>]\n"
"  --impute-sex ['max-female-fadj='<x>] ['min-male-fadj='<y>]\n"
"               ['max-female-ycount='<z>] ['min-male-ycount='<w>]\n"
"               ['max-female-yrate='<v>] ['min-male-yrate='<u>]\n"
"               ['cols='<column set descriptor>]\n"
"    --check-sex compares sex assignments in the input dataset with those\n"
"    imputed from chrX inbreeding coefficients and/or chrY valid genotype call\n"
"    count/rate (heterozygous genotype calls are invalid on chrY).\n"
"    Specifically:\n"
"    * If max-female-xf= and/or min-male-xf= are specified, chrX is used if\n"
"      present.\n"
"    * If at least one of the ycount/yrate thresholds are specified, chrY is\n"
"      used if present.\n"
"    * If both chrX and chrY are usable, sex is only called if both conditions\n"
"      are satisfied.  Similarly, if both count and rate are specified for chrY,\n"
"      the strictest condition must be satisfied.\n"
"    * If no thresholds are specified at all, a warning is printed, and then\n"
"      min-male-xf is set to 1 and max-female-yrate is set to 0.  In this case,\n"
"      unless you're just sanity-checking pre-cleaned data, you should look at\n"
"      the distributions of xf and yrate in the .sexcheck output file, and then\n"
"      rerun --check-sex with data-derived thresholds.\n"
"    Other notes:\n"
"    * Make sure that the chrX pseudo-autosomal region has been split off (with\n"
"      e.g. --split-par) before using this.\n"
"    * You also need decent MAF estimates (so, with very few samples in your\n"
"      immediate fileset, use --read-freq), and it's best for your variants to\n"
"      be in approximate Hardy-Weinberg and linkage equilibrium.\n"
"    * For samples which barely fail the max-female-xf threshold, you may want\n"
"      to check autosomal inbreeding coefficients (--het).  When that is also\n"
"      high, you're probably dealing with a highly-inbred female.\n"
"    * Supported column sets in the .sexcheck output file are:\n"
"        maybefid: FID, if that column was present in the input.\n"
"        fid: Force FID column to be written even when absent in the input.\n"
"        (IID is always present, and positioned here.)\n"
"        maybesid: SID, if that column was present in the input.\n"
"        sid: Force SID column to be written even when absent in the input.\n"
"        pedsex: Sex code in input file.\n"
"        (SNPSEX is always present, and positioned here.)\n"
"        status: 'OK' on non-NA pedsex=snpsex, otherwise 'PROBLEM'.\n"
"        xf: If chrX used, inbreeding coefficient estimated off chrX.\n"
"        ycount: If chrY used, number of valid chrY genotypes.\n"
"        yrate: If chrY used, chrY valid genotype rate.\n"
"        yobs: If chrY used, number of chrY variants considered.\n"
"      The default is maybefid,maybesid,pedsex,status,xf,yrate.\n"
"    --impute-sex changes sex assignments to the imputed values, and is\n"
"    otherwise identical to --check-sex.  It must be used with\n"
"    --make-[b]pgen/--make-bed/--export/--write-covar and no other commands.\n\n"
              );
    // possible todo: Patterson's adjacent-block jackknife tweak
    // (https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/jackcorr2.pdf )
    HelpPrint("fst\0Fst\0", &help_ctrl, 1,
"  --fst <categorical or binary phenotype name> ['method='<method name>]\n"
"        ['blocksize='<jackknife block size>] ['cols='<column set descriptor>]\n"
"        ['report-variants'] ['zs'] ['vcols='<column set descriptor>]\n"
"        ['base='<pop. ID> | 'ids='<pop. ID> | 'file='<pop.-ID-pair file>]\n"
"        [other population ID(s) for base=/ids=...]\n"
"    Estimate Wright's Fst between pairs of populations.\n"
"    * Two methods are supported:\n"
"      * 'hudson': Bhatia G, Patterson N, Sankararaman S, Price AL (2013)\n"
"                  Estimating and interpreting F_{ST}: The impact of rare\n"
"                  variants.  This is now the default.\n"
"      * 'wc': Weir BS, Cockerham CC (1984) Estimating F-statistics for the\n"
"              analysis of population structure.\n"
"      In both cases, the final estimate is a ratio-of-averages.\n"
"    * If chrX is present, its results are written to separate file(s) with \".x\"\n"
"      in the extension when the Hudson method is used.  (chrX is skipped under\n"
"      the Weir-Cockerham method.)\n"
"    * To get block-jackknife-based standard error estimates, provide a\n"
"      blocksize= value.\n"
"    * There is only one optional column set in the main summary:\n"
"        (POP1 and POP2 are always present, and positioned here.)\n"
"        nobs: Number of variants with valid Fst estimates.\n"
"        (HUDSON_FST or WC_FST is always present, and positioned here.)\n"
"        (SE is present if blocksize= specified, and positioned here.)\n"
"      nobs is not included by default.\n"
"    * You can request per-variant Fst estimates with the 'report-variants'\n"
"      modifier; this generates a separate output file for each population pair.\n"
"      Supported per-variant report column sets are:\n"
"        chrom: Chromosome ID.\n"
"        pos: Base-pair coordinate.\n"
"        (ID is always present, and positioned here.)\n"
"        ref: Reference allele.\n"
"        alt: All alternate alleles, comma-separated.\n"
"        maybeprovref: Reports whether REF allele is marked as known or\n"
"                      provisional, when at least one of the latter is present,\n"
"                      and the REF column is present.\n"
"        provref: Force provref column even if all-'N'.\n"
"        nobs: Number of (nonmissing) genotype observations across pop pair.\n"
"        nallele: Number of nonmissing alleles.\n"
"        fstfrac: Numerator and denominator of Fst estimate.\n"
"        fst: Fst estimate.\n"
"      The default is chrom,pos,maybeprovref,nobs,fst.\n"
"    * By default, all pairs of populations are compared.  If you only want to\n"
"      compare some pairs, there are three ways to do this.\n"
"      * base= specifies one base population to be compared with all others; or\n"
"        if you specify more population ID(s) afterward, just the other\n"
"        populations you've listed.\n"
"      * ids= specifies an all-vs.-all comparison within the given set of\n"
"        populations.\n"
"      * file= specifies a file containing one population pair per line.\n"
"      Note that 'base='/'ids='/'file=' must be positioned after all modifiers.\n\n"
              );
    HelpPrint("indep\0indep-pairwise\0indep-pairphase\0", &help_ctrl, 1,
"  --indep-pairwise <window size>['kb'] [step size (variant ct)]\n"
"                   <unphased-hardcall-r^2 threshold>\n"
"  --indep-pairphase <window size>['kb'] [step size (variant ct)]\n"
"                    <haplotype r^2 threshold>\n"
"    Generate a list of variants in approximate linkage equilibrium.\n"
"    * --indep-pairphase requires all genotypes to be phased, and performs a\n"
"      haplotype- instead of genotype-based calculation.\n"
"    * For multiallelic variants, major allele counts are used in the r^2\n"
"      computation.\n"
"    * With the 'kb' modifier, the window size is in kilobase instead of variant\n"
"      count units.  (Pre-'kb' space is optional, i.e.\n"
"      \"--indep-pairwise 500 kb 0.5\" and \"--indep-pairwise 500kb 0.5\" have the\n"
"      same effect.)\n"
"    * The step size now defaults to 1 if it's unspecified, and *must* be 1 if\n"
"      the window is in kilobase units.\n"
"    * Note that you need to rerun PLINK using --extract or --exclude on the\n"
"      .prune.in/.prune.out file to apply the list to another computation... and\n"
"      as with other applications of --extract/--exclude, duplicate variant IDs\n"
"      are a problem.  --indep-pairwise now errors out when duplicate variant\n"
"      IDs are present.\n\n"
              );
    HelpPrint("r-phased\0r-unphased\0r2-phased\0r2-unphased\0r\0r2\0", &help_ctrl, 1,
"  --r[2]-[un]phased [{square | square0 | triangle | inter-chr}] ['yes-really']\n"
"                    [{zs | bin | bin4}] ['ref-based']\n"
"                    ['allow-ambiguous-allele'] ['cols='<column set descriptor>]\n"
"    LD statistic reports.\n"
"    --r2-phased computes the textbook haplotype-frequency-based r^2, and\n"
"    corresponds to PLINK 1.9 --r2's behavior when the 'd', 'dprime', or\n"
"    'dprime-signed' modifier was present.  --r2-unphased computes the simpler\n"
"    r^2 squared-correlation between (unphased) dosage vectors, and corresponds\n"
"    to how PLINK 1.x --r2 behaved without a D'-related modifier.  You are now\n"
"    required to explicitly specify which of these r^2 statistics you want.\n"
"    --r-phased and --r-unphased report signed (and of course unsquared) values,\n"
"    with positive sign when the two major (or, when 'ref-based' is specified,\n"
"    REF) alleles are positively correlated with each other.\n"
"    Dosages are used when present.  (In the diploid case, an unphased dosage of\n"
"    x is interpreted as P(0/0) = 1 - x, P(0/1) = x when x is in 0..1.)\n"
"    Phase information is used when both variants are on the same chromosome.\n"
"    By default, tabular output is written to <output prefix>.vcor.\n"
"    * In this mode, the --ld-... flags filter the output.  \"--ld-window-kb\n"
"      1000\" and \"--ld-window-r2 0.2\" are active unless explicitly overridden.\n"
"    * To process inter-chromosomal as well as intra-chromosomal variant-pairs,\n"
"      use the 'inter-chr' modifier.\n"
"    * Supported column sets are:\n"
"        chrom: Two chromosome ID columns.\n"
"        pos: Two base-pair coordinate columns.\n"
"        id: Two variant ID columns.\n"
"        ref: Two reference-allele columns.\n"
"        alt1: Two alternate-allele-1 columns.\n"
"        alt: Two comma-separated-alternate-alleles columns.\n"
"        maybeprovref: Reports whether REF alleles are marked as known or\n"
"                      provisional, when at least one of the latter is present,\n"
"                      and the REF column-set is present.\n"
"        provref: Force provref columns even if all-'N'.\n"
"        maj: Two major-allele columns.\n"
"        nonmaj: Two comma-separated-nonmajor-alleles columns.\n"
"        freq: Two (1 - <major allele frequency>) columns.\n"
"        (r or r^2 is always present, and positioned here.)\n"
"        d: Coefficient of linkage disequilibrium (phased only).\n"
"        dprime: Lewontin's D' (phased only).\n"
"        dprimeabs: Absolute value of Lewontin's D' (phased only).\n"
"      The default is chrom,pos,id,maybeprovref for --r2-[un]phased; maj is also\n"
"      included for --r-[un]phased.\n"
"    * By default, when multiallelic variants are present, --r2-[un]phased will\n"
"      error out when the 'maj' and 'nonmaj' (or, if 'ref-based' is specified,\n"
"      'ref' and 'alt') column-sets are absent.  Similarly, --r-[un]phased will\n"
"      error out in these cases regardless of whether multiallelic variants are\n"
"      present.  The 'allow-ambiguous-allele' modifier overrides this behavior.\n"
"    To request all-pairs matrix output instead, specify a matrix shape\n"
"    ('square', 'square0', 'triangle') and/or encoding ('bin', 'bin4') modifier.\n"
"    * As with --make-rel and similar commands, if a shape is specified without\n"
"      an encoding, encoding defaults to text; and if an encoding is specified\n"
"      without a shape, shape defaults to square.\n"
"    * Since there is no header line specifying phased vs. unphased, r vs. r^2,\n"
"      or text vs. binary vs. Zstd-compressed-text, this information is embedded\n"
"      in the main matrix filename's extension.\n"
"      \".[un]phased.vcor{1,2}{|.bin|.zst}\" summarizes the twelve possibilities.\n"
"    * Since the resulting file can easily be huge, you're required to add the\n"
"      'yes-really' modifier when requesting an unfiltered, non-distributed\n"
"      all-pairs computation on more than 400k variants.\n"
"    With either output type, the computation can be subdivided with --parallel.\n\n"
              );
    HelpPrint("ld\0", &help_ctrl, 1,
"  --ld <variant ID> <variant ID> ['hwe-midp']\n"
"    This displays diplotype frequencies, haplotype-based r^2, and D' for a\n"
"    single pair of variants.  (The latter two values are calculated in the same\n"
"    manner as they are for --r2-phased.)\n"
"    When there is at least one sample with unphased het calls for both\n"
"    variants, diplotype frequencies are estimated using the Hill equation.  If\n"
"    there are multiple biologically possible local maxima, all are displayed,\n"
"    along with HWE exact test statistics.\n\n"
              );
    HelpPrint("sample-diff\0sdiff\0", &help_ctrl, 1,
"  --sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>]\n"
"                ['include-missing'] [{pairwise | counts-only}]\n"
"                ['fname-id-delim='<c>] ['zs'] ['cols='<column set descriptor>]\n"
"                ['counts-cols='<column set descriptor>]\n"
"                {base= | ids=}<sample ID> <other sample ID(s)...>\n"
"  --sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>]\n"
"                ['include-missing'] [{pairwise | counts-only}]\n"
"                ['fname-id-delim='<c>] ['zs'] ['cols='<column set descriptor>]\n"
"                ['counts-cols='<column set descriptor>] file=<ID-pair file>\n"
"    (alias: --sdiff)\n"
"    Report discordances and discordance-counts between pairs of samples.  If\n"
"    chrX or chrY is present, sex must be defined and consistent.\n"
"    * There are three ways to specify which sample pairs to compare.  To\n"
"      compare a single baseline sample against some others, start the\n"
"      (space-delimited) sample ID list with 'base='.  To perform an all-vs.-all\n"
"      comparison, start it with 'ids=' instead.  To compare sample pairs listed\n"
"      in a file, use 'file='.\n"
"      Note that 'base='/'ids='/'file=' must be positioned after all modifiers.\n"
"    * Sample IDs are interpreted as if they were in a VCF header line, with\n"
"      'id-delim=' having the usual effect.\n"
"    * By default, comparisons are based on hardcalls.  Use 'dosage' to compare\n"
"      dosages instead; you can combine this with a tolerance in [0, 0.5).\n"
"    * By default, if one genotype is missing and the other isn't, that doesn't\n"
"      count as a difference; this can be changed with 'include-missing'.\n"
"    * By default, a single main report is written to\n"
"      <output prefix>[.<base ID>].sdiff.  To write separate pairwise\n"
"      <output prefix>.<ID1>.<ID2>.sdiff reports for each compared ID pair, add\n"
"      the 'pairwise' modifier.  To omit the main report, add the 'counts-only'\n"
"      modifier.  (Note that, if you're only interested in nonmissing autosomal\n"
"      biallelic hardcalls, --make-king-table provides a more efficient way to\n"
"      compute just counts.)\n"
"    * By default, if an output filename has a multipart sample ID, the parts\n"
"      will be delimited by '_'; use 'fname-id-delim=' to change this.\n"
"    Supported main-report column sets are:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      (Variant ID is always present, and positioned here.)\n"
"      ref: Reference allele.\n"
"      alt: All alternate alleles, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present,\n"
"                    and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      maybefid: FID1/FID2, if that column was in the input.  Requires 'id'.\n"
"      fid: Force FID1/FID2 even when FID was absent in the input.\n"
"      id: IID1/IID2.\n"
"      maybesid: SID1/SID2, if that column was in the input.  Requires 'id'.\n"
"      sid: Force SID1/SID2 even when SID was absent in the input.\n"
"      geno: Unphased GT or DS for the two samples.\n"
"    The default is usually chrom,pos,ref,alt,maybeprovref,maybefid,id,maybesid,\n"
"    geno; the sample IDs are removed from the default in 'pairwise' mode.\n"
"    Supported discordance-count-summary column sets are:\n"
"      maybefid: FID1/FID2, if that column was in the input.\n"
"      fid: Force FID1/FID2 even when FID was absent in the input.\n"
"      (IID1/IID2 are always present.)\n"
"      maybesid: SID1/SID2, if that column was in the input.\n"
"      sid: Force SID1/SID2 even when SID was absent in the input.\n"
"      nobs: Number of variants considered.  This includes variants where one or\n"
"            both variants are missing iff 'include-missing' was specified.\n"
"      nobsibs: ibs0+ibs1+ibs2.\n"
"      ibs0: Number of diploid variants with no common hardcall alleles.\n"
"      ibs1: Number of diploid variants with exactly 1 common hardcall allele.\n"
"      ibs2: Number of diploid variants with both hardcall alleles matching.\n"
"      halfmiss: Number of variants with exactly 1 missing genotype/dosage.\n"
"                Ignored without 'include-missing'.\n"
"      diff: Total number of differences.\n"
"    The default is maybefid,maybesid,nobs,halfmiss,diff.\n\n"
              );
    // for kinship estimation, LD pruning isn't really advisable (if more speed
    // is needed, the humble --bp-space may lead to a better approximation?
    // and in practice speed doesn't seem to be an issue any more with
    // --make-king.)
    //
    // For multiallelic variants, major allele counts are theoretically
    // slightly more informative than REF allele counts, but the advantage is
    // far too small to be worth losing allele-frequency-independence.
    HelpPrint("make-king\0make-king-table\0", &help_ctrl, 0,
"  --make-king [{square | square0 | triangle}] [{zs | bin | bin4}]\n"
"    KING-robust kinship estimator, described by Manichaikul A, Mychaleckyj JC,\n"
"    Rich SS, Daly K, Sale M, Chen WM (2010) Robust relationship inference in\n"
"    genome-wide association studies.  By default, this writes a\n"
"    lower-triangular tab-delimited table of kinship coefficients to\n"
"    <output prefix>.king, and a list of the corresponding sample IDs to\n"
"    <output prefix>.king.id.  The first row of the .king file contains a single\n"
"    <genome 1-genome 2> kinship coefficient, the second row has the\n"
"    <genome 1-genome 3> and <genome 2-genome 3> kinship values in that order,\n"
"    etc.\n"
"    * Only autosomes are currently considered.\n"
"    * Pedigree information is currently ignored; the between-family estimator\n"
"      is used for all pairs.\n"
"    * For multiallelic variants, REF allele counts are used.\n"
"    * If the 'square' or 'square0' modifier is present, a square matrix is\n"
"      written instead; 'square0' fills the upper right triangle with zeroes.\n"
"    * If the 'zs' modifier is present, the .king file is Zstd-compressed.\n"
"    * If the 'bin' modifier is present, a binary (square) matrix of\n"
"      double-precision floating point values, suitable for loading from R, is\n"
"      instead written to <output prefix>.king.bin.  ('bin4' specifies\n"
"      single-precision numbers instead.)  This can be combined with 'square0'\n"
"      if you still want the upper right zeroed out, or 'triangle' if you don't\n"
"      want to pad the upper right at all.\n"
"    * The computation can be subdivided with --parallel.\n"
              );
    HelpPrint("make-king\0make-king-table\0genome\0", &help_ctrl, 1,
"  --make-king-table ['zs'] ['counts'] ['rel-check' | 'concordance-check']\n"
"                    ['cols='<col set descrip.>]\n"
"    Similar to --make-king, except results are reported in KING's original\n"
"    .kin0 text table format (with minor changes, e.g. row order is more\n"
"    friendly to incremental addition of samples).  'rel-check' restricts the\n"
"    calculation to same-FID pairs, while 'concordance-check' restricts to\n"
"    same-FID-and-IID.\n"
"    Supported column sets are:\n"
"      maybefid: FID1/FID2, if that column was in the input.  Requires 'id'.\n"
"      fid: Force FID1/FID2 even when FID was absent in the input.\n"
"      id: IID1/IID2.\n"
"      maybesid: SID1/SID2, if that column was in the input.  Requires 'id'.\n"
"      sid: Force SID1/SID2 even when SID was absent in the input.\n"
"      nsnp: Number of variants considered (autosomal, neither call missing).\n"
"      hethet: Proportion/count of considered call pairs which are het-het.\n"
"      ibs0: Proportion/count of considered call pairs which are opposite homs.\n"
"      ibs1: HET1_HOM2 and HET2_HOM1 proportions/counts.\n"
"      ibs: Hamming distance (2 * ibs0 + ibs1), / (2 * nsnp) if proportion.\n"
"      kinship: KING-robust between-family kinship estimator.\n"
"    The default is maybefid,id,maybesid,nsnp,hethet,ibs0,kinship.\n"
"    hethet/ibs0/ibs1 values are proportions unless the 'counts' modifier is\n"
"    present.  If id is omitted, a .kin0.id file is also written.\n\n"
               );
    // possible todo: --king-table-subset analogue for fast-approximate
    // --make-grm-sparse
    HelpPrint("make-rel\0make-grm\0make-grm-bin\0make-grm-list\0make-grm-gz\0make-grm-sparse\0", &help_ctrl, 1,
"  --make-rel ['cov'] ['meanimpute'] [{square | square0 | triangle}]\n"
"             [{zs | bin | bin4}]\n"
"    Write a lower-triangular variance-standardized relationship matrix to\n"
"    <output prefix>.rel, and corresponding IDs to <output prefix>.rel.id.\n"
"    * This computation assumes that variants do not have very low MAF, or\n"
"      deviate greatly from Hardy-Weinberg equilibrium.\n"
// depending on what your original variant set looks like, you can occasionally
// get a better variant-weighting without LD-pruning, but it's the right
// default recommendation
"    * Also, it's usually best to perform this calculation on a variant set in\n"
"      approximate linkage equilibrium.\n"
"    * The 'cov' modifier replaces the variance-standardization step with basic\n"
"      mean-centering, causing a covariance matrix to be calculated instead.\n"
"    * The computation can be subdivided with --parallel.\n"
"  --make-grm-list ['cov'] ['meanimpute'] ['zs'] [{id-header | iid-only}]\n"
"  --make-grm-bin ['cov'] ['meanimpute'] [{id-header | iid-only}]\n"
"    --make-grm-list causes the relationships to be written to GCTA's original\n"
"    list format, which describes one pair per line, while --make-grm-bin writes\n"
"    them in GCTA 1.1+'s single-precision triangular binary format.  Note that\n"
"    these formats explicitly report the number of valid observations (where\n"
"    neither sample has a missing call) for each pair, which is useful input for\n"
"    some scripts.\n"
"  --make-grm-sparse <threshold> ['cov'] ['meanimpute'] ['zs']\n"
"                    [{id-header | iid-only}]\n"
"    --make-grm-sparse generates a \"sparse GRM\" containing only relationship\n"
"    coefficients greater than or equal to the given threshold.\n\n"
               );
#ifndef NOLAPACK
    // GRM, PCA, etc. based on major vs. nonmajor alleles
    // possible todo: have an 'approx2' mode which implements the flashpca 2.0
    //   algorithm, which does not require memory quadratic in the # of PCs.
    //   but probably not, don't see any real application for that many PCs?
    HelpPrint("pca\0", &help_ctrl, 1,
"  --pca [count] [{approx | meanimpute}] ['scols='<col set descriptor>]\n"
"  --pca [{allele-wts | biallelic-var-wts}] [count] [{approx | meanimpute}]\n"
"        ['vzs'] ['scols='<col set descriptor>] ['vcols='<col set descriptor>]\n"
"    Extracts top principal components from the variance-standardized\n"
"    relationship matrix.\n"
"    * It is usually best to perform this calculation on a variant set in\n"
"      approximate linkage equilibrium, with no very-low-MAF variants.\n"
"    * By default, 10 PCs are extracted; you can adjust this by passing a\n"
"      numeric argument.  (Note that 10 is lower than the PLINK 1.9 default of\n"
"      20; this is due to the randomized algorithm's memory footprint growing\n"
"      quadratically w.r.t. the PC count.)\n"
"    * The 'approx' modifier causes the standard deterministic computation to be\n"
"      replaced with the randomized algorithm originally implemented for\n"
"      Galinsky KJ, Bhatia G, Loh PR, Georgiev S, Mukherjee S, Patterson NJ,\n"
"      Price AL (2016) Fast Principal-Component Analysis Reveals Convergent\n"
"      Evolution of ADH1B in Europe and East Asia.  This can be a good idea when\n"
"      you have >5k samples, and is almost required with >50k.\n"
"    * The randomized algorithm always uses mean imputation for missing genotype\n"
"      calls.  For comparison purposes, you can use the 'meanimpute' modifier to\n"
"      request this behavior for the standard computation.\n"
"    * 'scols=' can be used to customize how sample IDs appear in the .eigenvec\n"
"      file.  (maybefid, fid, maybesid, and sid supported; default is\n"
"      maybefid,maybesid.)\n"
"    * The 'allele-wts' modifier requests an additional one-line-per-allele\n"
"      .eigenvec.allele file with PCs expressed as allele weights instead of\n"
"      sample weights.  When it's present, 'vzs' causes the .eigenvec.allele\n"
"      file to be Zstd-compressed.\n"
"      'vcols=' can be used to customize the report columns; supported column\n"
"      sets are:\n"
"        chrom: Chromosome ID.\n"
"        pos: Base-pair coordinate.\n"
"        (ID is always present, and positioned here.)\n"
"        ref: Reference allele.\n"
"        alt1: Alternate allele 1.\n"
"        alt: All alternate alleles, comma-separated.\n"
"        maybeprovref: Reports whether REF allele is marked as known or\n"
"                      provisional, when at least one of the latter is present,\n"
"                      and the REF column is present.\n"
"        provref: Force provref column even if all-'N'.\n"
"        (A1 is always present, and positioned here.)\n"
"        ax: Non-A1 alleles, comma-separated.\n"
"        (PCs are always present, and positioned here.)\n"
"      Default is chrom,ref,alt,maybeprovref.\n"
"    * For datasets with no multiallelic variants, the 'biallelic-var-wts'\n"
"      modifier requests the old .eigenvec.var format, which only reports\n"
"      weights for major alleles.  (These weights are 2x the corresponding\n"
"      .eigenvec.allele weights.)  Supported column sets are:\n"
"        chrom: Chromosome ID.\n"
"        pos: Base-pair coordinate.\n"
"        (ID is always present, and positioned here.)\n"
"        ref: Reference allele.\n"
"        alt1: Alternate allele 1.\n"
"        alt: All alternate alleles, comma-separated.\n"
"        maybeprovref: Reports whether REF allele is marked as known or\n"
"                      provisional, when at least one of the latter is present,\n"
"                      and the REF column is present.\n"
"        provref: Force provref column even if all-'N'.\n"
"        maj: Major allele.\n"
"        nonmaj: Minor allele.\n"
"        (PCs are always present, and positioned here.  Signs are w.r.t. the\n"
"        major, not necessarily reference, allele.)\n"
"      Default is chrom,maybeprovref,maj,nonmaj.\n\n"
               );
#endif
    HelpPrint("king-cutoff\0king-cutoff-table\0make-king\0make-king-table\0rel-cutoff\0grm-cutoff\0", &help_ctrl, 1,
"  --king-cutoff [.king.bin + .king.id fileset prefix] <threshold>\n"
"  --king-cutoff-table <.kin0 filename> <threshold>\n"
"    Exclude one member of each pair of samples with KING-robust kinship greater\n"
"    than the given threshold.  Remaining/excluded sample IDs are written to\n"
"    <output prefix>.king.cutoff.in.id + .king.cutoff.out.id.\n"
"    * If a .king.bin file is provided to --king-cutoff, it must be triangular\n"
"      (either precision is ok).\n"
"    * The .kin0 file provided to --king-cutoff-table must contain sample ID\n"
"      columns.\n\n"
               );
    HelpPrint("write-covar\0with-phenotype\0", &help_ctrl, 1,
"  --write-covar ['cols='<column set descriptor>]\n"
"    If covariates are defined, an updated version (with all filters applied) is\n"
"    automatically written to <output prefix>.cov whenever --make-pgen,\n"
"    --make-just-psam, --export, or a similar command is present.  However, if\n"
"    you do not wish to simultaneously generate a new sample file, you can use\n"
"    --write-covar to just produce a pruned covariate file.\n"
"    Supported column sets are:\n"
"      maybefid: FID, if that column was in the input.\n"
"      fid: Force FID column to be written even when absent in the input.\n"
"      maybesid: SID, if that column was in the input.\n"
"      sid: Force SID column to be written even when absent in the input.\n"
"      maybeparents: Father/mother IIDs ('0' = missing), if columns in input.\n"
"      parents: Force PAT/MAT columns to be written even when absent in input.\n"
"      sex: '1' = male, '2' = female, 'NA' = missing.\n"
"      pheno1: First active phenotype.  If none, all column entries are set to\n"
"              the --output-missing-phenotype string.\n"
"      phenos: All active phenotypes, if any.  (Can be combined with pheno1 to\n"
"              force at least one phenotype column to be written.)\n"
"      (Covariates are always present, and positioned here.)\n"
"    The default is maybefid,maybesid.\n\n"
               );
    HelpPrint("pmerge\0pmerge-list\0merge\0merge-list\0bmerge\0", &help_ctrl, 1,
"  --pmerge <.pgen/.bed filename> <.pvar/.bim> <.psam/.fam>\n"
"  --pmerge <.pgen + .pvar + .psam fileset prefix> ['vzs']\n"
"    Merge the given fileset with the initially loaded fileset, writing the\n"
"    result to <output prefix>.pgen + .pvar + .psam.\n"
"  --pmerge-list <filename> [mode]\n"
"    Merge all filesets named in the text file.  Also merge with the initially\n"
"    loaded fileset if one was specified.\n"
"    When a line in the text file contains three entries, they are interpreted\n"
"    as full filenames for a binary fileset (.pgen/.bed, then .pvar/.bim, then\n"
"    .psam/.fam).  If it contains exactly one entry, its interpretation depends\n"
"    on the mode:\n"
"    * 'bfile': Prefix for .bed + .bim + .fam fileset.\n"
"    * 'bpfile': Prefix for .pgen + .bim + .fam fileset.\n"
"    * 'pfile' (default): Prefix for .pgen + .pvar + .psam fileset.\n"
"    * 'pfile-vzs': Prefix for .pgen + .pvar.zst + .psam fileset.\n"
"    For both --pmerge and --pmerge-list:\n"
"    * All input filesets must be sorted by position, and have the same\n"
"      chromosome order.  (When this isn't true, use --make-pgen + --sort-vars\n"
"      on each fileset first.)\n"
"    * Variants are only merged if their IDs AND positions match.  (This is a\n"
"      change from PLINK 1.x.)\n\n"
              );
    HelpPrint("pgen-diff\0merge-mode\0", &help_ctrl, 1,
"  --pgen-diff <.pgen/.bed filename> <.pvar/.bim> <.psam/.fam>\n"
"              ['include-missing'] ['zs'] ['dosage' | 'dosage='<tolerance>]\n"
"              ['cols='<column set descriptor>]\n"
"  --pgen-diff <.pgen + .pvar + .psam prefix> ['vzs'] ['include-missing'] ['zs']\n"
"              ['dosage' | 'dosage='<tolerance>] ['cols='<col set descriptor>]\n"
"    Report unphased genotype/dosage differences in the intersection of two\n"
"    filesets.  (Sample and variant filters are also applied.)\n"
"    * If chrX or chrY is present, sex must be defined and consistent.\n"
"    * Variants are only compared if their IDs AND positions match.  An error\n"
"      is reported if any such match is not unique.\n"
"    * By default, comparisons are based on hardcalls.  Use 'dosage' to compare\n"
"      dosages instead; you can combine this with a tolerance in [0, 0.5).\n"
"    * By default, if one genotype is missing and the other isn't, that doesn't\n"
"      count as a difference; this can be changed with 'include-missing'.\n"
"    Supported column sets are:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      id: Variant ID.\n"
"      ref: Reference allele.\n"
"      alt: All alternate alleles across both filesets, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present,\n"
"                    and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      maybefid: FID, if that column was present in the input.\n"
"      fid: Force FID column to be written even when absent in the input.\n"
"      (IID is always present, and positioned here.)\n"
"      maybesid: SID, if that column was present in the input.\n"
"      sid: Force SID column to be written even when absent in the input.\n"
"      geno: Unphased GT or DS.\n"
"    The default is id,maybeprovref,maybefid,maybesid,geno.\n\n"
              );
    HelpPrint("write-samples\0write-snplist\0", &help_ctrl, 1,
"  --write-samples\n"
"    Report IDs of all samples which pass your filters/inclusion thresholds.\n\n"
               );
    HelpPrint("write-snplist\0", &help_ctrl, 1,
"  --write-snplist ['zs'] ['allow-dups']\n"
"    List all variants which pass your filters/inclusion thresholds.  Unless the\n"
"    'allow-dups' modifier is provided, this now errors out when duplicate\n"
"    variant ID(s) remain.\n\n"
               );
    HelpPrint("glm\0linear\0logistic\0assoc\0", &help_ctrl, 1,
"  --glm ['zs'] ['omit-ref'] [{sex | no-x-sex}] ['log10'] ['pheno-ids']\n"
"        [{genotypic | hethom | dominant | recessive | hetonly}] ['interaction']\n"
"        ['hide-covar'] ['skip-invalid-pheno'] ['allow-no-covars']\n"
"        ['qt-residualize'] [{intercept | cc-residualize | firth-residualize}]\n"
"        ['single-prec-cc'] [{no-firth | firth-fallback | firth}]\n"
"        ['cols='<col set desc>] ['local-covar='<file>] ['local-psam='<file>]\n"
"        ['local-pos-cols='<key col #s> | 'local-pvar='<file>] ['local-haps']\n"
"        ['local-omit-last' | 'local-cats[0]='<category ct>]\n"
"        ['aperm' | 'mperm='<value>] ['perm-count'] ['perm-cols='<col set desc>]\n"
"        ['permute-qt-residuals']\n"
"    Basic association analysis on quantitative and/or case/control phenotypes.\n"
"    For each variant, a linear (for quantitative traits) or logistic (for\n"
"    case/control) regression is run with the phenotype as the dependent\n"
"    variable, and nonmajor allele dosage(s) and a constant-1 column as\n"
"    predictors.\n"
"    * There is usually an additive effect line for every nonmajor allele, and\n"
"      no such line for the major allele.  To omit REF alleles instead of major\n"
"      alleles, add the 'omit-ref' modifier.  (When performing interaction\n"
"      testing, this tends to cause the multicollinearity check to fail for\n"
"      low-ref-frequency variants.)\n"
"    * By default, sex (male = 1, female = 2; note that this is a change from\n"
"      PLINK 1.x) is automatically added as a predictor for X chromosome\n"
"      variants, and no others.  The 'sex' modifier causes it to be added\n"
"      everywhere (except chrY), while 'no-x-sex' excludes it entirely.\n"
"    * The 'log10' modifier causes p-values to be reported in -log10(p) form.\n"
"    * 'pheno-ids' causes the samples used in each set of regressions to be\n"
"      written to an .id file.  (When the samples differ on chrX or chrY, .x.id\n"
"      and/or .y.id files are also written.)\n"
"    * The 'genotypic' modifier adds an additive effect/dominance deviation 2df\n"
"      joint test (0-2 and 0..1..0 coding), while 'hethom' uses 0..0..1 and\n"
"      0..1..0 coding instead.  If permutation is also requested, these\n"
"      modifiers cause permutation to be based on the joint test.\n"
"    * 'dominant' and 'recessive' specify a model assuming full dominance or\n"
"      recessiveness, respectively, for the ref allele.  I.e. the genotype\n"
"      column is recoded as 0..1..1 or 0..0..1, respectively.\n"
"    * 'hetonly' replaces the genotype column with a dominance-deviation column.\n"
// 'interaction' now ok with permutation
"    * 'interaction' adds genotype x covariate interactions to the model.  Note\n"
"      that this tends to produce 'NA' results (due to the multicollinearity\n"
"      check) when the reference allele is 'wrong'; --maj-ref can be used to\n"
"      enable analysis of those variants.\n"
"    * Additional predictors can be added with --covar.  By default, association\n"
"      statistics are reported for all nonconstant predictors; 'hide-covar'\n"
"      suppresses covariate-only results, while 'intercept' causes intercepts\n"
"      to be reported.\n"
"      Since running --glm without at least e.g. principal component covariates\n"
"      is usually an analytical mistake, the 'allow-no-covars' modifier is now\n"
"      required when you're intentionally running --glm without a covariate\n"
"      file.\n"
"    * By default, if the current phenotype and covariates are such that every\n"
"      regression on a chromosome will fail, PLINK 2 errors out.  To just skip\n"
"      the phenotype or chromosome instead, add the 'skip-invalid-pheno'\n"
"      modifier.\n"
"    * There are now three regression modes for case/control phenotypes:\n"
"      * 'no-firth' requests PLINK 1.x's behavior, where a NA result is reported\n"
"        when basic logistic regression fails to converge.\n"
"      * 'firth-fallback' requests logistic regression, followed by Firth\n"
"        regression whenever the logistic regression fails to converge.  This is\n"
"        now the default.\n"
"      * 'firth' requests Firth regression all the time.\n"
"    * To trade off some accuracy for speed:\n"
"      * You can use the 'single-prec-cc' modifier to request use of\n"
"        single-precision instead of double-precision floating-point numbers\n"
"        during logistic and Firth regression.\n"
"      * You can use the 'firth-residualize' or 'cc-residualize' modifier, which\n"
"        implements the shortcut described in Mbatchou J et al. (2021)\n"
"        Computationally efficient whole genome regression for quantitative and\n"
"        binary traits.  Similarly, you can use 'qt-residualize' to regress out\n"
"        covariates upfront for quantitative traits.  (These must be used with\n"
"        'hide-covar', and disable some other --glm features.)\n"
"    * To add covariates which are not constant across all variants, add the\n"
"      'local-covar=' and 'local-psam=' modifiers, use full filenames for each,\n"
"      and use either 'local-pvar=' or 'local-pos-cols=' to provide variant ID\n"
"      or position information.\n"
"      Normally, the local-covar file should have c * n real-valued columns,\n""      where the first c columns correspond to the first sample in the\n"
"      local-psam file, columns (c+1) to 2c correspond to the second sample,\n"
"      etc.; and the mth line corresponds to the mth nonheader line of the\n"
"      local-pvar file when there is one.  (Variants outside of the local-pvar\n"
"      file are excluded from the regression.)  The local covariates are\n"
"      assigned the names LOCAL1, LOCAL2, etc.; to exclude the last local\n"
"      covariate from the regression (necessary if they are e.g. local ancestry\n"
"      coefficients which sum to 1), add 'local-omit-last'.\n"
"      Alternatively, with 'local-cats='<k>, the local-covar file is expected to\n"
"      have n columns with integer-valued entries in [1, k].  (This range is\n"
"      [0, k-1] with 'local-cats0='.)  These category assignments are expanded\n"
"      into (k-1) local covariates in the usual manner.\n"
"      When position information is in the local-covar file, this should be\n"
"      indicated by 'local-pos-cols='<number of header rows>,<chrom col #>,<pos\n"
"      start col #>,<first covariate col #>.\n"
"      'local-haps' indicates that there's one column or column-group per\n"
"      haplotype instead of per sample; they are averaged by --glm.\n"
"    * 'aperm' normally causes an adaptive permutation test to be performed on\n"
"      the main effect, while 'mperm='<value> starts a max(T) permutation test.\n"
"    * 'perm-count' causes the permutation test report to include counts instead\n"
"      of frequencies.\n"
"    * For quantitative phenotypes, 'permute-qt-residuals' causes permutation to\n"
"      occur on phenotype residuals instead of the original phenotype.\n"
// Original set-based test not worth keeping.  Probable todo: review current
// rare-variant and gene-based testing methods.
"    The main report supports the following column sets:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      (ID is always present, and positioned here.)\n"
"      ref: Reference allele.\n"
"      alt1: Alternate allele 1.\n"
"      alt: All alternate alleles, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present,\n"
"                    and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      (A1 is always present, and positioned here.  For multiallelic variants,\n"
"      this column may contain multiple comma-separated alleles when the result\n"
"      doesn't depend on which allele is A1.)\n"
"      omitted: Omitted allele.\n"
"      ax: Non-A1 alleles, comma-separated.  Deprecated (use 'omitted' instead).\n"
"      a1count: A1 allele count (can be decimal with dosage data).\n"
"      totallele: Allele observation count (can be higher than --freq value, due\n"
"                 to inclusion of het haploids and chrX model).\n"
"      a1countcc: A1 count in cases, then controls (case/control only).\n"
"      totallelecc: Case and control allele observation counts.\n"
"      gcountcc: Genotype hardcall counts (neither-A1, het-A1, A1-A1) in cases,\n"
"                then controls (case/control only).\n"
"      a1freq: A1 allele frequency.  This will be added to the default column\n"
"              set in the future.\n"
"      a1freqcc: A1 frequency in cases, then controls (case/control only).\n"
"      machr2: Unphased MaCH imputation quality (frequently labeled 'INFO').\n"
"      firth: Reports whether Firth regression was used (firth-fallback only).\n"
"      test: Test identifier.  (Required unless only one test is run.)\n"
"      nobs: Number of samples in the regression.\n"
"      beta: Regression coefficient (for A1 if additive test).\n"
"      orbeta: Odds ratio for case/control, beta for quantitative traits.\n"
"              (Ignored if 'beta' column set included.)\n"
"      se: Standard error of beta.\n"
"      ci: Bounds of symmetric approximate confidence interval (requires --ci).\n"
"      tz: T-statistic for linear regression, Wald Z-score for logistic/Firth.\n"
"      p: Asymptotic p-value (or -log10(p)) for T/Z-statistic.\n"
"      err: Error code for NA results.\n"
"    The default is chrom,pos,ref,alt,provref,omitted,a1freq,firth,test,nobs,\n"
"    orbeta,se,ci,tz,p,err.\n"
"    Permutation reports support the chrom, pos, ref, alt[1], [maybe]provref,\n"
"    and omitted column sets; their default is\n"
"    chrom,ref,alt,maybeprovref,omitted.\n\n"
               );
    HelpPrint("gwas-ssf\0glm\0linear\0logistic\0assoc\0", &help_ctrl, 1,
"  --gwas-ssf ['zs'] ['delete-orig-glm'] ['a1freq-lower-limit='<bound>]\n"
"             ['rsid='<mode>] ['file='<filename>] ['file-list='<filename>]\n"
"             [{real-ref-alleles | allow-ambiguous-indels}]\n"
"    Reformat PLINK 2 association test results as GWAS-SSF, for the GWAS Catalog\n"
"    (https://www.ebi.ac.uk/gwas/ ).  Output files have '.ssf.tsv' appended\n"
"    to the original filenames.\n"
"    * You will need to prepare companion metadata file(s).\n"
"    * If --glm was specified, --gwas-ssf will postprocess --glm's results, and\n"
"      optionally delete the --glm results afterward ('delete-orig-glm'\n"
"      modifier).\n"
"    * To postprocess some preexisting file(s), use file= and/or file-list= .\n"
"      Note that these files must contain most default column sets, including\n"
"      'a1freq' (so PLINK 1.x --linear/--logistic output is not supported).\n"
"      * By default, unless the 'provref' column is present in the input file,\n"
"        true REF alleles are assumed to be unknown, since --glm is sometimes\n"
"        run on PLINK 1 filesets which don't track that information.  Use the\n"
"        'real-ref-alleles' modifier to specify that REF alleles are accurate.\n"
"    * For indels, REF alleles are normally *required* to be known, because\n"
"      (unlike the case for SNPs) swapping REF/ALT order for an indel actually\n"
"      changes the genetic variation that is referred to.  If --gwas-ssf errors\n"
"      out for this reason, but you have an upstream VCF or similar file from\n"
"      which the correct REF/ALT allele labels can be recovered (see the\n"
"      --ref-allele flag documentation for details), you are STRONGLY encouraged\n"
"      to recover those labels.\n"
"      If it's genuinely impossible to recover them, you can use the\n"
"      'allow-ambiguous-indels' modifier to override the error.  In this case,\n"
"      some of your indel results will probably be unusable.\n"
"    * Variants outside {chr1..chr22, chrX, chrY, chrM}, and variants with\n"
"      non-ACGT characters in the A1 or OMITTED allele code, are skipped.  (The\n"
"      PAR1, PAR2, and XY chromosome codes are converted to chrX.)\n"
"    * If the 'omitted' column is absent from an input file, --gwas-ssf will\n"
"      skip (unsplit) multiallelic variants.\n"
"      Conversely, if unsplit multiallelic variants and the 'omitted' column are\n"
"      present, the multiallelic variants will be handled properly, and the\n"
"      results should be more reliable than what you'd get from splitting the\n"
"      variants.  Specify \"other minor alleles\" (or \"other ALT alleles\" if you\n"
"      ran with 'omit-ref') as part of the \"adjustedCovariates\" metadata entry\n"
"      in this case.\n"
"    * By default, a 'rsid' column appears in the output iff at least one\n"
"      variant in the current dataset has an ID that is a syntactically valid\n"
"      rsID (mode='infer').  Modes 'no' and 'yes' do what they say.\n"
"    * You can use the 'a1freq-lower-limit=' modifier to mask very low allele\n"
"      frequencies, when the raw values would compromise privacy.\n\n"
              );
#ifndef NOLAPACK
    HelpPrint("pheno-svd\0glm\0", &help_ctrl, 1,
"  --pheno-svd <# output phenotypes> ['force'] ['scols='<col set descriptor>]\n"
"                                    ['pcols='<col set descriptor>]\n"
"  --pheno-svd variance=<#> ['force'] ['scols='<col set descriptor>]\n"
"                           ['pcols='<col set descriptor>]\n"
"    Perform SVD of full rows (i.e. samples with no missing phenotype values) of\n"
"    the phenotype matrix, generate new phenotypes (named 'SVDPHENO1',\n"
"    'SVDPHENO2', etc.) equal to the top left-singular vectors, and save them to\n"
"    <output prefix>.svd.pheno.  Singular values + input-phenotype weights are\n"
"    written to <output prefix>.svd.pheno_wts.\n"
"    By default, if less than half of the remaining samples have full phenotype\n"
"    rows, this command errors out.  In this case, you may want to use a method\n"
"    like softImpute (https://cran.r-project.org/web/packages/softImpute/ ) to\n"
"    fill in some missing phenotype values, possibly after excluding some\n"
"    nonessential phenotypes with an especially large number of missing values.\n"
"    Alternatively, you can use 'force' to override the error; this usually\n"
"    isn't the best idea.\n"
"    Other notes:\n"
"    * The first argument determines the number of new phenotypes to generate.\n"
"      You can either directly specify a number, or use 'variance=' to specify\n"
"      how much variance in the original phenotype matrix they must explain.\n"
"    * A mix of binary and quantitative phenotypes is permitted.  Binary\n"
"      phenotypes are encoded as control=0, case=1 before the SVD is performed.\n"
"    * If there are any later commands in the same run (e.g. --glm), they will\n"
"      only see the newly-generated phenotypes.\n"
"    * 'scols=' can be used to customize how sample IDs appear in the .svd.pheno\n"
"      file.  (maybefid, fid, maybesid, and sid supported; default is\n"
"      maybefid,maybesid.)\n"
"    * 'pcols=' can be used to customize the .svd.pheno_wts file; supported\n"
"      column sets are:\n"
"        id: New phenotype ID.\n"
"        sv: Singular value.\n"
"        (Old phenotypes are always present, and positioned here.)\n"
"      Default is id,sv.\n\n"
              );
#endif
    HelpPrint("clump\0", &help_ctrl, 1,
"  --clump ['zs'] ['cols='<col set desc>] <PLINK report filename(s)...>\n"
"    Postprocess --glm and similar association analysis report(s), organizing\n"
"    results into LD-based clumps.  Multiple filenames can be separated by\n"
"    spaces or commas.  Dosages are used in the LD computations.\n"
"    Supported column sets are:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      (ID is always present, and positioned here.)\n"
"      ref: Reference allele.\n"
"      alt1: Alternate allele 1.\n"
"      alt: All alternate alleles, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present,\n"
"                    and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      maybea1: A1 allele, if at least 1 multiallelic index variant is present.\n"
"      a1: Force A1 column even if all index variants are biallelic.\n"
"      maybef: 1-based file number, if more than one file is provided.\n"
"      f: Force F column (and SP2 entry) even when only one file is provided.\n"
"      (P is always present, and positioned here.)\n"
"      total: Number of other variants in clump.\n"
"      maybebounds: If --clump-range[0] specified, bp range of members with p <\n"
"                   --clump-p2 threshold (two cols).\n"
"      bounds: Force bp range columns even without --clump-range[0].\n"
"      bins: Number of clumped variants in each p-value bin.\n"
"      sp2: IDs, and possibly A1 allele and/or file number, of members with p <\n"
"           --clump-p2 threshold.\n"
"      (Overlapping-range names always present and positioned here if\n"
"       --clump-range[0] specified)\n"
"    The default is chrom,pos,maybeprovref,maybea1,maybef,total,maybebounds,\n"
"    bins,sp2.\n\n"
              );
    HelpPrint("score\0score-list\0", &help_ctrl, 1,
"  --score <filename> [i] [j] [k] [{header | header-read}]\n"
"                     [{center | variance-standardize | dominant | recessive}]\n"
"                     ['no-mean-imputation'] ['se'] ['zs'] ['ignore-dup-ids']\n"
"                     [{list-variants | list-variants-zs}]\n"
"                     ['cols='<col set descriptor>]\n"
"  --score-list <fnm> [i] [j] [k] [{header | header-read}]\n"
"                     [{center | variance-standardize | dominant | recessive}]\n"
"                     ['no-mean-imputation'] ['se'] ['zs'] ['ignore-dup-ids']\n"
"                     ['cols='<col set descriptor>]\n"
"    Apply linear scoring system(s) to each sample.\n"
"    For --score-list, the input file should contain a list of filenames; each\n"
"    of those files is then processed as if it were passed to --score, then\n"
"    results are merged together.\n"
"    The rest of this section describes --score.\n"
"    * The input file should have one line per scored (variant, allele) pair.\n"
"      Variant IDs are read from column #i and allele codes are read from column\n"
"      #j, where i defaults to 1 and j defaults to i+1.\n"
"    * By default, a single column of input coefficients is read from column #k,\n"
"      where k defaults to j+1.  (--score-col-nums can be used to specify\n"
"      multiple columns.)\n"
"    * 'header-read' causes the first line of the input file to be treated as a\n"
"      header line containing score names.  Otherwise, score(s) are assigned the\n"
"      names 'SCORE1', 'SCORE2', etc.; and 'header' just causes the first line\n"
"      to be entirely ignored.\n"
"    * By default, copies of unnamed alleles contribute zero to score, while\n"
"      missing genotypes contribute an amount proportional to the loaded (via\n"
"      --read-freq) or imputed allele frequency.  To throw out missing\n"
"      observations instead (decreasing the denominator in the final average\n"
"      when this happens), use the 'no-mean-imputation' modifier.\n"
"    * You can use the 'center' modifier to shift all genotypes to mean zero, or\n"
"      'variance-standardize' to linearly transform the genotypes to mean-0,\n"
"      variance-1.\n"
"    * The 'dominant' modifier causes dosages greater than 1 to be treated as 1,\n"
"      while 'recessive' uses max(dosage - 1, 0) on diploid chromosomes.\n"
"      ('dominant', 'recessive', and 'variance-standardize' cannot be used with\n"
"      chrX.)\n"
"    * The 'se' modifier causes the input coefficients to be treated as\n"
"      independent standard errors; in this case, standard errors for the score\n"
"      average/sum are reported, under a Gaussian approximation.  (Note that\n"
"      this will systematically underestimate standard errors when scored\n"
"      variants are in LD.)\n"
"    * By default, --score errors out if a variant ID in the input file appears\n"
"      multiple times in the main dataset.  Use the 'ignore-dup-ids' modifier to\n"
"      skip them instead (a warning is still printed if such variants are\n"
"      present).\n"
"    * The 'list-variants[-zs]' modifier causes variant IDs used for scoring to\n"
"      be written to <output prefix>.sscore.vars[.zst].\n"
"    The main --score report supports the following column sets:\n"
"      maybefid: FID, if that column was in the input.\n"
"      fid: Force FID column to be written even when absent in the input.\n"
"      (IID is always present, and positioned here.)\n"
"      maybesid: SID, if that column was in the input.\n"
"      sid: Force SID column to be written even when absent in the input.\n"
"      pheno1: First active phenotype.\n"
"      phenos: All active phenotypes, if any.\n"
"      nallele: Number of nonmissing alleles.\n"
"      denom: Denominator of score average (equal to nallele value when\n"
"             'no-mean-imputation' specified).\n"
"      dosagesum: Sum of named allele dosages.\n"
"      scoreavgs: Score averages.\n"
"      scoresums: Score sums.\n"
"    The default is maybefid,maybesid,phenos,nallele,dosagesum,scoreavgs.\n"
"    --score-list is the same, except the nallele/denom/dosagesum column sets\n"
"    are unavailable.\n"
"    For more sophisticated polygenic risk scoring, we recommend looking at the\n"
"    LDpred2 (https://privefl.github.io/bigsnpr/articles/LDpred2.html ) and\n"
"    PRSice-2 (https://www.prsice.info/ ) software packages.\n\n"
               );
    HelpPrint("variant-score\0vscore\0", &help_ctrl, 1,
"  --variant-score <filename> ['bin' | 'bin4' | 'cols='<col set descriptor>]\n"
"                  ['zs'] ['single-prec']\n"
"    (alias: --vscore)\n"
"    Apply linear scoring system(s) to each variant.  Each reported variant\n"
"    score is the dot product of a sample-weight vector with the\n"
"    total-ALT-dosage vector, with MAF-based mean imputation applied to missing\n"
"    dosages.\n"
"    Input file format: one line per sample, each starting with an ID and\n"
"    followed by scoring weight(s); it can also have a header line with the\n"
"    sample ID representation and the score name(s).\n"
"    The usual .vscore text report supports the following column sets:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      (ID is always present, and positioned here.)\n"
"      ref: Reference allele.\n"
"      alt1: Alternate allele 1.\n"
"      alt: All alternate alleles, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present,\n"
"                    and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      altfreq: ALT allele frequency used for mean-imputation.\n"
"      nmiss: Number of missing (and thus mean-imputed) dosages.\n"
"      nobs: Number of (nonmissing) sample observations.\n"
"      (Variant scores are always present, and positioned here.)\n"
"    Default is chrom,pos,ref,alt,maybeprovref.\n"
"    If binary output is requested instead, the main .vscore.bin matrix contains\n"
"    floating-point values, column (score) ID(s) are saved to\n"
"    <output prefix>.vscore.cols, and variant IDs are saved to\n"
"    <output prefix>.vscore.vars[.zst].\n"
"    'single-prec' causes the computation to use single- instead of\n"
"    double-precision floating-point values internally.\n\n"
              );
    HelpPrint("adjust-file\0adjust\0", &help_ctrl, 1,
"  --adjust-file <filename> ['zs'] ['gc'] ['cols='<column set descriptor>]\n"
"                ['log10'] ['input-log10'] ['test='<test name, case-sensitive>]\n"
"    Given a file with unfiltered association test results, report some basic\n"
"    multiple-testing corrections, sorted in increasing-p-value order.\n"
"    * 'gc' causes genomic-controlled p-values to be used in the formulas.\n"
"      (This tends to be overly conservative.  We note that LD Score regression\n"
"      usually does a better job of calibrating lambda; see Lee JJ, McGue M,\n"
"      Iacono WG, Chow CC (2018) The accuracy of LD Score regression as an\n"
"      estimator of confounding and genetic correlations in genome-wide\n"
"      association studies.)\n"
"    * 'log10' causes negative base 10 logs of p-values to be reported, instead\n"
"      of raw p-values.  'input-log10' specifies that the input file contains\n"
"      -log10(p) values.\n"
"    * If the input file contains multiple tests per variant which are\n"
"      distinguished by a 'TEST' column (true for --linear/--logistic/--glm),\n"
"      you must use 'test=' to select the test to process.\n"
"    The following column sets are supported:\n"
"      chrom: Chromosome ID.\n"
"      pos: Base-pair coordinate.\n"
"      (ID is always present, and positioned here.)\n"
"      ref: Reference allele.\n"
"      alt1: Alternate allele 1.\n"
"      alt: All alternate alleles, comma-separated.\n"
"      maybeprovref: Reports whether REF allele is marked as known or\n"
"                    provisional, when at least one of the latter is present,\n"
"                    and the REF column is present.\n"
"      provref: Force provref column even if all-'N'.\n"
"      a1: Tested allele.  (Omitted if missing from input file.)\n"
"      unadj: Unadjusted p-value.\n"
"      gc: Devlin & Roeder (1999) genomic control corrected p-value (additive\n"
"          models only).\n"
"      qq: P-value quantile.\n"
"      bonf: Bonferroni correction.\n"
"      holm: Holm-Bonferroni (1979) adjusted p-value.\n"
"      sidakss: Sidak single-step adjusted p-value.\n"
"      sidaksd: Sidak step-down adjusted p-value.\n"
"      fdrbh: Benjamini & Hochberg (1995) step-up false discovery control.\n"
"      fdrby: Benjamini & Yekutieli (2001) step-up false discovery control.\n"
"    Default set is chrom,maybeprovref,a1,unadj,gc,bonf,holm,sidakss,sidaksd,\n"
"    fdrbh,fdrby.\n\n"
               );
    // todo: reimplement most/all of PLINK 1.x's other automatic checks (het
    // haploids, missing sex, etc. with corresponding output files) and have a
    // flag (--qc1?) which invokes them all.
    HelpPrint("genotyping-rate\0", &help_ctrl, 1,
"  --genotyping-rate ['dosage']\n"
"    Report genotyping rate in log (this was automatic in PLINK 1.x).\n\n"
               );
    HelpPrint("pgen-info\0", &help_ctrl, 1,
"  --pgen-info\n"
"    Reports basic information about a .pgen file.\n\n"
               );
    HelpPrint("validate\0", &help_ctrl, 1,
"  --validate\n"
"    Validates all variant records in a .pgen file.\n\n"
               );
    HelpPrint("zst-decompress\0zd\0", &help_ctrl, 1,
"  --zst-decompress <.zst file> [output filename]\n"
"    (alias: --zd)\n"
"    Decompress a Zstd-compressed file.  If no output filename is specified, the\n"
"    file is decompressed to standard output.\n"
"    This cannot be used with any other flags, and does not cause a log file to\n"
"    be generated.\n\n"
               );
    if (!param_ct) {
      fputs(
"The following other flags are supported.\n"
// tbd: document order of operations
, stdout);
    }
    HelpPrint("script\0rerun\0", &help_ctrl, 0,
"  --script <fname>    : Include command-line options from file.\n"
"  --rerun [log]       : Rerun commands in log (default 'plink2.log').\n"
               );
    HelpPrint("version\0", &help_ctrl, 0,
"  --version           : Display only version number before exiting.\n"
               );
    HelpPrint("silent\0", &help_ctrl, 0,
"  --silent            : Suppress regular output to console.  (Error-output is\n"
"                        not suppressed.)\n"
               );
    HelpPrint("vcf\0bcf\0bgen\0double-id\0const-fid\0id-delim\0", &help_ctrl, 0,
"  --double-id         : When importing single-part sample IDs, set both FID and\n"
"                        IID to the original ID.\n"
"  --const-fid [ID]    : When importing single-part sample IDs, set FID to the\n"
"                        given constant and IID to the original ID.\n"
"  --id-delim [d]      : Normally parses single-delimiter sample IDs as\n"
"                        <FID><d><IID>, and double-delimiter IDs as\n"
"                        <FID><d><IID><d><SID>; default delimiter is '_'.\n"
"                        --id-delim can no longer be used with\n"
"                        --double-id/--const-fid; it will error out if any ID\n"
"                        lacks the delimiter.\n"
               );
    HelpPrint("idspace-to\0vcf\0bcf\0bgen\0id-delim\0vcf-idspace-to\0", &help_ctrl, 0,
"  --idspace-to <char> : Convert spaces in VCF/.bgen/.ind sample IDs to the\n"
"                        given character.\n"
               );
    HelpPrint("iid-sid\0id-delim\0sample-diff\0indv\0", &help_ctrl, 0,
"  --iid-sid           : Make --id-delim, --indv, and --sample-diff interpret\n"
"                        two-token sample IDs as IID-SID instead of FID-IID.\n"
              );
    HelpPrint("vcf\0bcf\0vcf-half-call\0vcf-min-gq\0vcf-min-dp\0vcf-max-dp\0vcf-require-gt\0vcf-ploidy\0vcf-ref-n-missing\0", &help_ctrl, 0,
"  --vcf-require-gt    : Skip variants with no GT field.\n"
"  --vcf-min-gq <val>  : No-call genotypes when GQ is present and below the\n"
"                        threshold.\n"
"  --vcf-max-dp <val>  : No-call genotypes when DP is present and above/below\n"
"  --vcf-min-dp <val>    the threshold.\n"
"  --vcf-half-call <m> : Specify how '0/.' and similar VCF GT values should be\n"
"                        handled.  The following four modes are supported:\n"
"                        * 'error'/'e' (default) errors out and reports line #.\n"
"                        * 'haploid'/'h' treats them as haploid calls.\n"
"                        * 'missing'/'m' treats them as missing.\n"
"                        * 'reference'/'r' treats the missing value as 0.\n"
"  --vcf-ref-n-missing : Import VCF 'N' REF alleles as missing alleles.  This\n"
"                        can be appropriate for .ped-derived VCFs.\n"
               );
    HelpPrint("vcf\0vcf-allow-no-nonvar\0", &help_ctrl, 0,
"  --vcf-allow-no-nonvar : By default, --vcf without dosage= errors out when\n"
"                          given a single-sample file with no 0, 0/0, or 0|0 GT\n"
"                          values among 1000+ scanned variants with non-missing\n"
"                          GT, since that implies the VCF was not generated\n"
"                          properly (e.g. GATK GenotypeGVCFs was run without\n"
"                          --include-non-variant-sites).  --vcf-allow-no-nonvar\n"
"                          suppresses this error.\n"
              );
    HelpPrint("oxford-single-chr\0data\0gen\0bgen\0", &help_ctrl, 0,
"  --oxford-single-chr <chr name>  : Specify single-chromosome .gen/.bgen file\n"
"                                    with no useful chromosome info inside.\n"
               );
    HelpPrint("lax-bgen-import\0bgen\0", &help_ctrl, 0,
"  --lax-bgen-import               : Do not error out when .bgen header has an\n"
"                                    overstated variant count (possible from\n"
"                                    IMPUTE5).\n"
              );
    HelpPrint("missing-code\0missing_code\0data\0sample\0", &help_ctrl, 0,
"  --missing-code [string list]    : Comma-delimited list of missing phenotype\n"
"    (alias: --missing_code)         values for Oxford-format import (default\n"
"                                    'NA').\n"
               );
    // any need to keep --hard-call-threshold random?  postpone it for now...
    HelpPrint("hard-call-threshold\0gen\0bgen\0data\0import-dosage\0", &help_ctrl, 0,
"  --hard-call-threshold <val>     : When importing dosage data, a hardcall is\n"
"                                    normally saved when the distance from the\n"
"                                    nearest hardcall, defined as\n"
"                                      0.5 * sum_i |x_i - round(x_i)|\n"
"                                    (where the x_i's are 0..2 allele dosages),\n"
"                                    is not greater than 0.1.  You can adjust\n"
"                                    this threshold by providing a numeric\n"
"                                    argument to --hard-call-threshold.\n"
"                                    You can also use this with --make-[b]pgen\n"
"                                    to alter the saved hardcalls while leaving\n"
"                                    the dosages untouched, or --make-bed to\n"
"                                    tweak hardcall export.\n"
               );
    HelpPrint("dosage-erase-threshold\0import-dosage-certainty\0gen\0bgen\0data\0vcf\0bcf\0import-dosage\0", &help_ctrl, 0,
"  --dosage-erase-threshold <val>  : --hard-call-threshold normally preserves\n"
"                                    the original dosages, and several PLINK 2\n"
"                                    commands use them when they're available.\n"
"                                    Use --dosage-erase-threshold to make PLINK\n"
"                                    2 erase dosages and keep only hardcalls\n"
"                                    when distance-from-hardcall <= the given\n"
"                                    level.\n"
"  --import-dosage-certainty <val> : The PLINK 2 file format currently supports\n"
"                                    a single dosage for each allele.  Some\n"
"                                    other dosage file formats include a\n"
"                                    separate probability for every possible\n"
"                                    genotype, e.g. {P(0/0)=0.2, P(0/1)=0.52,\n"
"                                    P(1/1)=0.28}, a highly uncertain call that\n"
"                                    is nevertheless treated as a hardcall under\n"
"                                    '--hard-call-threshold 0.1'.  To make PLINK\n"
"                                    2 treat a dosage as missing whenever the\n"
"                                    largest probability is less than a\n"
"                                    threshold, use --import-dosage-certainty.\n"
               );
    HelpPrint("input-missing-genotype\0missing-genotype\0", &help_ctrl, 0,
"  --input-missing-genotype <c> : '.' is always interpreted as a missing\n"
"                                 genotype code in input files.  By default, '0'\n"
"                                 also is; you can change this second missing\n"
"                                 code with --input-missing-genotype.\n"
               );
    HelpPrint("strict-extra-chr\0allow-extra-chr\0aec\0", &help_ctrl, 0,
"  --strict-extra-chr      : Prohibit unrecognized chromosome codes, unless\n"
"                            --allow-extra-chr is also specified.\n"
"  --allow-extra-chr ['0'] : Explicitly permit unrecognized chromosome codes.\n"
"    (alias: --aec)          The '0' modifier causes these codes to be converted\n"
"                            to \"0\".\n"
               );
    // possible todo: nonhuman PARs?
    HelpPrint("chr-set\0cow\0dog\0horse\0hound\0mouse\0rice\0sheep\0autosome-num\0human\0chr-override\0", &help_ctrl, 0,
"  --chr-set <autosome ct> ['no-x'] ['no-y'] ['no-xy'] ['no-mt'] :\n"
"    Specify a nonhuman chromosome set.  The first parameter sets the number of\n"
"    diploid autosome pairs if positive, or haploid chromosomes if negative.\n"
"    Given diploid autosomes, the remaining modifiers indicate the absence of\n"
"    the named non-autosomal chromosomes.\n"
"  --cow/--dog/--horse/--mouse/--rice/--sheep : Shortcuts for those species.\n"
"  --autosome-num <val>    : Alias for '--chr-set <value> no-y no-xy no-mt'.\n"
"  --human                 : Explicitly specify human chromosome set, and make\n"
"                            output .pvar/VCF files include a ##chrSet header\n"
"                            line.  (.pvar/VCF output files automatically\n"
"                            include ##chrSet when a nonhuman set is specified.)\n"
"  --chr-override ['file'] : By default, if --chr-set/--autosome-num/--cow/etc.\n"
"                            conflicts with an input file ##chrSet header line,\n"
"                            PLINK 2 will error out.  --chr-override with no\n"
"                            argument causes the command line to take\n"
"                            precedence; '--chr-override file' defers to the\n"
"                            file.\n"
               );
    // possible todo: --var-max-qual
    HelpPrint("var-min-qual\0var-filter\0vcf-min-qual\0vcf-filter\0qual-scores\0qual-threshold\0qual-max-threshold\0", &help_ctrl, 0,
"  --var-min-qual <val>             : Skip variants with low/missing QUAL.\n"
"  --var-filter [exception(s)...]   : Skip variants which have FILTER failures.\n"
               );
    HelpPrint("extract-if-info\0exclude-if-info\0require-info\0require-no-info\0extract-if\0exclude-if\0keep-if-info\0remove-if-info\0var-min-qual\0var-filter\0vcf-min-qual\0vcf-filter\0", &help_ctrl, 0,
"  --extract-if-info <expr...> : Exclude variants which don't/do satisfy a\n"
"  --exclude-if-info <expr...>   boolean expression on INFO key(s), e.g.\n"
"  (aliases: --extract-if,         --extract-if-info '(VT==SNP)&&(999<DP<99999)'\n"
"            --exclude-if)       As a special case, a value of ';' specifies the\n"
"                                empty-string.\n"
"                                Unless the operator is !=, a predicate always\n"
"                                evaluates to false when the key is missing.\n"
"  --require-info <key(s)...>  : Exclude variants based on nonexistence or\n"
"  --require-no-info <k...>      existence of an INFO key.  \"<key>=.\" is treated\n"
"                                as nonexistence.\n"
              );
    HelpPrint("extract-col-cond\0extract-col-cond-match\0extract-col-cond-mismatch\0extract-col-cond-substr\0extract-col-cond-min\0extract-col-cond-max\0extract-fcol\0extract-fcol-match\0extract-fcol-mismatch\0extract-fcol-substr\0extract-fcol-min\0extract-fcol-max\0qual-scores\0qual-threshold\0qual-max-threshold\0attrib\0", &help_ctrl, 0,
"  --extract-col-cond <f> [valcol] [IDcol] [skip] :\n"
"  --extract-col-cond-match <(sub)string(s)...>\n"
"  --extract-col-cond-mismatch <(sub)string(s)...>\n"
"  --extract-col-cond-substr\n"
"  --extract-col-cond-min <min>\n"
"  --extract-col-cond-max <max> :\n"
"    Exclude all variants without a value-column entry satisfying a condition.\n"
"    * By default, values are read from column 2 of the file, and variant IDs\n"
"      are read from column 1.\n"
"    * Three types of conditions are supported:\n"
"      * When --extract-col-cond-match is specified without\n"
"        --extract-col-cond-substr, the value is checked for equality with the\n"
"        given strings, and kept iff one of them matches.  Similarly,\n"
"        --extract-col-cond-mismatch without --extract-col-cond-substr causes\n"
"        the variant to be kept iff the value matches none of the given strings.\n"
"      * When --extract-col-cond-match and/or -mismatch are specified with\n"
"        --extract-col-cond-substr, the variant is kept iff none of the\n"
"        --extract-col-cond-mismatch substrings are contained in the value, and\n"
"        either --extract-col-cond-match was unspecified or at least one of its\n"
"        substrings is contained.\n"
"      * Otherwise, the value is interpreted as a number, and the variant is\n"
"        kept if the number is in [<min>, <max>] (default min=0, max=DBL_MAX).\n"
              );
    HelpPrint("pheno\0pheno-name\0pheno-col-nums\0not-pheno\0mpheno\0phenoExcludeList\0", &help_ctrl, 0,
"  --pheno ['iid-only'] <f> : Specify additional phenotype/covariate file.\n"
"                             Comma-delimited files with a header line are now\n"
"                             permitted.\n"
"  --pheno-name <name...>   : Only load the designated phenotype(s) from the\n"
"                             --pheno (if one was specified) or .psam (if no\n"
"                             --pheno) file.  Separate multiple names with\n"
"                             spaces or commas, and use dashes to designate\n"
"                             ranges.\n"
"  --pheno-col-nums <#...>  : Only load the phenotype(s) in the designated\n"
"                             column number(s) from the --pheno file.\n"
"  --not-pheno <name...>    : Ignore the named phenotype(s).\n"
               );
    HelpPrint("bfile\0fam\0psam\0no-psam-pheno\0no-fam-pheno\0no-pheno\0pheno\0pheno-name\0", &help_ctrl, 0,
"  --no-psam-pheno          : Ignore phenotype(s) in .psam/.fam file.\n"
               );
    HelpPrint("strict-sid0\0", &help_ctrl, 0,
"  --strict-sid0      : By default, if there is no SID column in the .psam/.fam\n"
"                       (or --update-ids) file, but there is one in another\n"
"                       input file (for e.g. --keep/--remove), the latter SID\n"
"                       column is ignored; sample IDs are considered matching as\n"
"                       long as FID and IID are equal (with missing FID treated\n"
"                       as '0').  If you also want to require SID = '0' for a\n"
"                       sample ID match in this situation, add --strict-sid0.\n"
              );
    HelpPrint("no-categorical\0input-missing-phenotype\0no-input-missing-phenotype\0pheno\0covar\0", &help_ctrl, 0,
"  --no-categorical   : Force all non-numeric phenotype/covariate strings to be\n"
"                       interpreted as missing values, not category names.\n"
              );
    // bugfix (27 Feb 2019): "\01" is interpreted as a single character, not a
    // null followed by a '1'...
    HelpPrint("input-missing-phenotype\0no-input-missing-phenotype\0neg9-pheno-really-missing\0\061\0missing-catname\0missing-phenotype\0", &help_ctrl, 0,
"  --input-missing-phenotype <v> : Set nonzero number to treat as a missing\n"
"                                  pheno/covar in input files (default -9).\n"
"  --no-input-missing-phenotype  : Don't treat any nonzero number as a missing\n"
"                                  pheno/covar.  ('NA'/'nan' are still treated\n"
"                                  as missing.)\n"
"  --neg9-pheno-really-missing   : When neither --input-missing-phenotype nor\n"
"                                  --no-input-missing-phenotype are specified,\n"
"                                  and a pheno/covar value in [-8, -9) or\n"
"                                  (-9, -10] is present, PLINK 2 now errors out\n"
"                                  when -9 is also present: in this context it\n"
"                                  is too likely that -9 does not represent a\n"
"                                  missing value.\n"
"                                  --neg9-pheno-really-missing suppresses the\n"
"                                  error.\n"
"  --1                           : Expect case/control phenotypes in input files\n"
"                                  and the command line to be coded as 0 =\n"
"                                  control, 1 = case, instead of the usual 0 =\n"
"                                  missing, 1 = ctrl, 2 = case.\n"
"                                  (Unlike PLINK 1.x, this does not force all\n"
"                                  phenotypes to be interpreted as case/ctrl.)\n"
"  --missing-catname <str>       : Set missing-categorical-phenotype string\n"
"                                  (case-sensitive, default 'NONE').\n"
               );
    HelpPrint("covar\0covar-name\0covar-col-nums\0not-covar\0covar-number\0covarExcludeList\0", &help_ctrl, 0,
"  --covar ['iid-only'] <f> : Specify additional covariate file.\n"
"                             Comma-delimited files with a header line are now\n"
"                             permitted.\n"
"  --covar-name <name...>   : Only load the designated covariate(s) from the\n"
"                             --covar (if one was specified), --pheno (if no\n"
"                             --covar), or .psam (if no --covar or --pheno)\n"
"                             file.\n"
"  --covar-col-nums <#...>  : Only load the covariate(s) in the designated\n"
"                             column number(s) from the --covar (if one was\n"
"                             specified) or --pheno (if no --covar) file.\n"
"  --not-covar <name...>    : Ignore the named covariate(s).\n"
               );
    HelpPrint("within\0mwithin\0family\0family-missing-catname\0", &help_ctrl, 0,
"  --within <f> [new pheno name] : Import a PLINK 1.x categorical phenotype.\n"
"                                  (Phenotype name defaults to 'CATPHENO'.)\n"
"                                  * If any numeric values are present, ALL\n"
"                                    values must be numeric.  In that case, 'C'\n"
"                                    is added in front of all category names.\n"
"                                  * 'NA' is treated as a missing value.\n"
"  --mwithin <n>                 : Load --within categories from column n+2.\n"
"  --family [new pheno name]     : Create a categorical phenotype from FID.\n"
"                                  Restrictions on and handling of numeric\n"
"                                  values are the same as for --within.\n"
"  --family-missing-catname <nm> : Make --family treat the specified FID as\n"
"                                  missing.\n"
               );
    HelpPrint("keep\0remove\0keep-fam\0remove-fam\0samples-file\0", &help_ctrl, 0,
"  --keep <fname...>    : Exclude all samples not named in a file.\n"
"  --remove <fname...>  : Exclude all samples named in a file.\n"
"  --keep-fam <fn...>   : Exclude all families not named in a file.\n"
"  --remove-fam <f...>  : Exclude all families named in a file.\n"
               );
    HelpPrint("extract\0exclude\0range\0extract-intersect\0regions-file\0", &help_ctrl, 0,
"  --extract [{bed0 | bed1}] <f...> : Usually excludes all variants (not) named\n"
"  --exclude [{bed0 | bed1}] <f...>   in the given file(s).  When multiple files\n"
"                                     are named, they are concatenated.\n"
"                                     With the 'bed0' or 'bed1' modifier,\n"
"                                     variants outside/inside the positional\n"
"                                     ranges in the interval-BED file(s) are\n"
"                                     excluded instead.  'bed0' tells PLINK 2 to\n"
"                                     assume the interval bounds follow the UCSC\n"
"                                     0-based half-open convention, while 'bed1'\n"
"                                     (equivalent to PLINK 1.9 'range')\n"
"                                     specifies 1-based fully-closed.\n"
               );
    HelpPrint("extract-intersect\0extract\0exclude\0", &help_ctrl, 0,
"  --extract-intersect [{bed0 | bed1}] <f...> : Just like --extract, except that\n"
"                                               a variant must be in the\n"
"                                               intersection, rather than just\n"
"                                               the union, of the files to\n"
"                                               remain.\n"
              );
    HelpPrint("bed-border-bp\0bed-border-kb\0make-set-border\0extract\0exclude\0extract-intersect\0range\0", &help_ctrl, 0,
"  --bed-border-bp <n>      : Stretch BED intervals by the given amount on each\n"
"  --bed-border-kb <n>        side.\n"
              );
    HelpPrint("keep-cats\0keep-cat-names\0keep-cat-pheno\0remove-cats\0remove-cat-names\0remove-cat-pheno\0keep-clusters\0keep-cluster-names\0remove-clusters\0remove-cluster-names\0", &help_ctrl, 0,
"  --keep-cats <filename>   : These can be used individually or in combination\n"
"  --keep-cat-names <nm...>   to define a list of categories to keep; all\n"
"                             samples not in one of the named categories are\n"
"                             excluded.  Use spaces to separate category names\n"
"                             for --keep-cat-names.  Use the --missing-catname\n"
"                             value (default 'NONE') to refer to the group of\n"
"                             uncategorized samples.\n"
"  --keep-cat-pheno <pheno> : If more than one categorical phenotype is loaded,\n"
"                             or you wish to filter on a categorical covariate,\n"
"                             --keep-cat-pheno must be used to specify which\n"
"                             phenotype/covariate --keep-cats and\n"
"                             --keep-cat-names apply to.\n"
"  --remove-cats <filename> : Exclude all categories named in the file.\n"
"  --remove-cat-names <...> : Exclude named categories.\n"
"  --remove-cat-pheno <phe> : Specify pheno for --remove-cats/remove-cat-names.\n"
               );
    HelpPrint("split-cat-pheno\0dummy-coding\0", &help_ctrl, 0,
"  --split-cat-pheno [{omit-most | omit-last}] ['covar-01']\n"
"                    [cat. pheno/covar name(s)...] :\n"
"    Split n-category phenotype(s) into n (or n-1, with 'omit-most'/'omit-last')\n"
"    binary phenotypes, with names of the form <orig. pheno name>=<cat. name>.\n"
"    (As a consequence, affected phenotypes and categories are not permitted to\n"
"    contain the '=' character.)\n"
"    * This happens after all sample filters.\n"
"    * If no phenotype or covariate names are provided, all categorical\n"
"      phenotypes (but not covariates) are processed.\n"
"    * By default, generated covariates are coded as 1=false, 2=true.  To code\n"
"      them as 0=false, 1=true instead, add the 'covar-01' modifier.\n"
               );
    HelpPrint("loop-cats\0loop-assoc\0", &help_ctrl, 0,
"  --loop-cats <pheno/covar>   : Run variant filters and subsequent operations\n"
"                                on just the samples in the first category; then\n"
"                                just the samples in the second category; and so\n"
"                                on, for all categories in the named categorical\n"
"                                phenotype.\n"
               );
    HelpPrint("no-id-header\0write-samples\0king-cutoff\0", &help_ctrl, 0,
"  --no-id-header ['iid-only'] : Don't include a header line in .id output\n"
"                                files.  This normally forces two-column FID/IID\n"
"                                output; add 'iid-only' to force just\n"
"                                single-column IID.\n"
              );
    HelpPrint("variance-standardize\0covar-variance-standardize\0quantile-normalize\0pheno-quantile-normalize\0covar-quantile-normalize\0standard-beta\0glm\0linear\0logistic\0", &help_ctrl, 0,
"  --variance-standardize [pheno/covar name(s)...]\n"
"  --covar-variance-standardize [covar name(s)...] :\n"
"    Linearly transform named covariates (and quantitative phenotypes, if\n"
"    --variance-standardize) to mean-zero, variance 1.  If no arguments are\n"
"    provided, all possible phenotypes/covariates are affected.\n"
"    This is frequently necessary to prevent the multicollinearity check from\n"
"    failing when dealing with covariates where abs(mean) is much larger than\n"
"    the standard deviation, such as year of birth.\n"
"  --quantile-normalize [...]       : Force named covariates and quantitative\n"
"  --pheno-quantile-normalize [...]   phenotypes to a N(0,1) distribution,\n"
"  --covar-quantile-normalize [...]   preserving only the original rank orders.\n"
               );
    HelpPrint("chr\0not-chr\0", &help_ctrl, 0,
"  --chr <chr(s)...>  : Exclude all variants not on the given chromosome(s).\n"
"                       Valid choices for humans are 0 (unplaced), 1-22, X, Y,\n"
"                       XY, MT, PAR1, and PAR2.  Separate multiple chromosomes\n"
"                       with spaces and/or commas, and use a dash (no adjacent\n"
"                       spaces permitted) to denote a range, e.g.\n"
"                       '--chr 1-4, 22, par1, x, par2'.\n"
"  --not-chr <...>    : Reverse of --chr (exclude variants on listed\n"
"                       chromosomes).\n"
               );
    HelpPrint("autosome\0autosome-par\0autosome-xy\0chr\0not-chr\0", &help_ctrl, 0,
"  --autosome         : Exclude all non-autosomal variants.\n"
"  --autosome-par     : Exclude all non-autosomal variants, except those in a\n"
"                       pseudo-autosomal region.\n"
               );
    HelpPrint("snps-only\0", &help_ctrl, 0,
"  --snps-only ['just-acgt']  : Exclude non-SNP variants.  By default, SNP = all\n"
"                               allele codes are single-character (so\n"
"                               multiallelic variants with a mix of SNPs and\n"
"                               non-SNPs are excluded; split your variants first\n"
"                               if that's a problem).\n"
"                               The 'just-acgt' modifier restricts SNP codes to\n"
"                               {A,C,G,T,a,c,g,t,<missing>}.\n"
               );
    HelpPrint("exclude-palindromic-snps\0", &help_ctrl, 0,
"  --exclude-palindromic-snps : Exclude A/T and C/G biallelic SNPs.\n"
              );
    // best to only support --chr with --from-bp/--to-bp/etc., now that
    // FinalizeChrset() is deferred
    HelpPrint("from\0to\0snp\0window\0from-bp\0to-bp\0from-kb\0to-kb\0from-mb\0to-mb\0exclude-snp\0extract-snp\0", &help_ctrl, 0,
"  --from <var ID>    : Use ID(s) to specify a variant range to load.  When used\n"
"  --to   <var ID>      together, both variants must be on the same chromosome.\n"
"                       (--snps can be used to specify intervals which cross\n"
"                       chromosome boundaries.)\n"
"  --snp  <var ID>    : Specify a single variant to load.\n"
"  --exclude-snp <ID> : Specify a single variant to exclude.\n"
"  --window  <kbs>    : With --snp/--exclude-snp, loads/excludes all variants\n"
"                       within half the specified kb distance of the named one.\n"
"  --from-bp <pos>    : Use base-pair coordinates to define a variant range to\n"
"  --to-bp   <pos>      load.\n"
"  --from-kb <pos>      * You must use these with --chr, specifying a single\n"
"  --to-kb   <pos>        chromosome.\n"
"  --from-mb <pos>      * Decimals and negative numbers are permitted.\n"
"  --to-mb   <pos>      * The --to-bp(/-kb/-mb) position is no longer permitted\n"
"                         to be smaller than the --from-bp position.\n"
               );
    HelpPrint("snps\0exclude-snps\0ld-snps\0", &help_ctrl, 0,
"  --snps <var IDs...>  : Use IDs to specify variant range(s) to load or\n"
"  --exclude-snps <...>   exclude.  E.g. '--snps rs1111-rs2222, rs3333, rs4444'.\n"
               );
    HelpPrint("force-intersect\0extract\0extract-intersect\0from\0to\0snp\0from-bp\0to-bp\0from-kb\0to-kb\0from-mb\0to-mb\0extract-snp\0snps\0", &help_ctrl, 0,
"  --force-intersect    : PLINK 2 normally errors out when multiple variant\n"
"                         inclusion filters (--extract, --extract-col-cond,\n"
"                         --extract-intersect, --from/--to, --from-bp/--to-bp,\n"
"                         --snp, --snps) are specified.  --force-intersect\n"
"                         allows the run to proceed; the set intersection will\n"
"                         be taken.\n"
               );
    HelpPrint("indv\0keep\0samples\0", &help_ctrl, 0,
"  --indv <sample ID>   : Filter out all samples except for those matching\n"
"                         the provided sample ID.  (Separate the parts of a\n"
"                         multipart sample ID with spaces.)\n"
              );
    HelpPrint("thin\0thin-count\0", &help_ctrl, 0,
"  --thin <p>           : Randomly remove variants, retaining each with prob. p.\n"
"  --thin-count <n>     : Randomly remove variants until n of them remain.\n"
               );
    HelpPrint("bp-space\0thin\0", &help_ctrl, 0,
"  --bp-space <bps>     : Remove variants so that each pair is no closer than\n"
"                         the given bp distance.\n"
               );
    HelpPrint("thin-indiv\0thin-indiv-count\0max-indv\0", &help_ctrl, 0,
"  --thin-indiv <p>       : Randomly remove samples, retaining with prob. p.\n"
"  --thin-indiv-count <n> : Randomly remove samples until n of them remain.\n"
               );
    HelpPrint("keep-col-match\0keep-col-match-name\0keep-col-match-num\0keep-fcol\0keep-fcol-name\0keep-fcol-num\0filter\0mfilter\0", &help_ctrl, 0,
"  --keep-col-match <f> <val(s)...> : Exclude all samples without a 3rd column\n"
"                                     entry in the given file exactly matching\n"
"                                     one of the given strings.  (Separate\n"
"                                     multiple strings with spaces.)\n"
"  --keep-col-match-name <col name> : Check column with given name instead.\n"
"  --keep-col-match-num <n>         : Check nth column instead.\n"
               );
    HelpPrint("geno\0mind\0oblig-clusters\0oblig-missing\0", &help_ctrl, 0,
"  --geno [val] [{dosage | hh-missing}]\n"
"  --mind [val] [{dosage | hh-missing}] : \n"
"    Exclude variants (--geno) and/or samples (--mind) with missing call\n"
"    frequencies greater than a threshold (default 0.1).  (Note that the default\n"
"    threshold is only applied if --geno/--mind is invoked without an argument;\n"
"    when --geno/--mind is not invoked, no missing call frequency ceiling is\n""    enforced at all.  Other inclusion/exclusion default thresholds work the\n"
"    same way.)\n"
"    By default, when a dosage is present but a hardcall is not, the genotype is\n"
"    treated as missing; add the 'dosage' modifier to treat this case as\n"
"    nonmissing.  Alternatively, you can use 'hh-missing' to also treat\n"
"    heterozygous haploid calls as missing.\n"
               );
    HelpPrint("y-nosex-missing-stats\0genotyping-rate\0missing\0geno\0mind\0", &help_ctrl, 0,
"  --y-nosex-missing-stats : On chrY, include unknown-sex samples when computing\n"
"                            missing-genotype and heterozygous-haploid stats.\n"
              );
    HelpPrint("select-sid-representatives\0", &help_ctrl, 0,
"  --select-sid-representatives [missingness mode] <tiebreak mode>\n"
"                               ['parents-only'] :\n"
"    For each group of samples with matching FID+IID, filter out all but one.\n"
"    * This normally keeps the sample with the lowest missing call rate.  There\n"
"      are four missingness modes:\n"
"      'hc'/'hardcall' (default): Look at hardcalls (i.e. when a dosage is\n"
"                                 present but a hardcall is not, the call is\n"
"                                 considered to be missing).\n"
"      'hh-missing': Same as above, except heterozygous haploid hardcalls are\n"
"                    also treated as missing.\n"
"      'dosage': Treat both cases discussed above as nonmissing.\n"
"      'sid-only': Ignore missing call rate, just use SID.\n"
"    * The following SID-based tiebreak modes are supported:\n"
"      'first': Natural-sort SIDs and keep the first one.\n"
"      'first-ascii': ASCII-sort SIDs and keep the first one.\n"
"      'last': Natural-sort SIDs and keep the last one.\n"
"      'last-ascii': Natural-sort SIDs and keep the last one.\n"
"    * With 'parents-only', this filter is only applied to parents.\n"
              );
    /*
    HelpPrint("oblig-clusters\0oblig-missing\0", &help_ctrl, 0,
"  --oblig-missing <f1> <f2> : Specify blocks of missing genotype calls for\n"
"                              --geno/--mind to ignore.  The first file should\n"
"                              have variant IDs in the first column and block\n"
"                              IDs in the second, while the second file should\n"
"                              have FIDs in the first column, IIDs in the\n"
"                              second, and block IDs in the third.\n"
               );
    */
    HelpPrint("require-pheno\0require-covar\0keep-if\0remove-if\0prune\0", &help_ctrl, 0,
"  --require-pheno [name(s)...] : Remove samples missing any of the named\n"
"  --require-covar [name(s)...]   phenotype(s)/covariate(s).  If no arguments\n"
"                                 are provided, all phenotype(s)/covariate(s)\n"
"                                 must be present.\n"
               );
    // 'major' mode intentionally omitted since it's almost entirely redundant,
    // and kind of forces the underlying flag to be renamed
    HelpPrint("maf\0min-af\0max-maf\0max-af\0mac\0min-ac\0max-mac\0max-ac\0", &help_ctrl, 0,
"  --maf [freq] [mode]     : Exclude variants with allele frequency lower than a\n"
"    (alias: --min-af)       threshold (default 0.01).  By default, the nonmajor\n"
"                            allele frequency is used; the other supported modes\n"
"                            are 'nref' (non-reference), 'alt1', and 'minor'\n"
"                            (least frequent).  bcftools freq:mode notation is\n"
"                            permitted.\n"
"  --max-maf <freq> [mode] : Exclude variants with MAF greater than the\n"
"    (alias: --max-af)       threshold.\n"
"  --mac <ct> [mode]       : Exclude variants with allele dosage lower than the\n"
"    (alias: --min-ac)       given threshold.\n"
"  --max-mac <ct> [mode]   : Exclude variants with allele dosage greater than\n"
"    (alias: --max-ac)       the given threshold.\n"
               );
    HelpPrint("af-pseudocount\0maf-succ\0", &help_ctrl, 0,
"  --af-pseudocount <x>    : Given j observations of one allele and k\n"
"                            observations of the other for a biallelic variant,\n"
"                            infer allele frequencies of (j+x) / (j+k+2x) and\n"
"                            (k+x) / (j+k+2x), rather than the default j / (j+k)\n"
"                            and k / (j+k).\n"
"                            * For multiallelic variants, note that this makes\n"
"                              unobserved ALT alleles matter.\n"
"                            * This does not affect --freq's output.\n"
               );
    HelpPrint("max-alleles\0min-alleles\0biallelic-only\0", &help_ctrl, 0,
"  --min-alleles <ct> : Exclude variants with fewer than the given # of alleles.\n"
"                       (When a variant has exactly one ALT allele, and it's\n"
"                       a missing-code, it's excluded by \"--min-alleles 2\".)\n"
"  --max-alleles <ct> : Exclude variants with more than the given # of alleles.\n"
              );
    HelpPrint("import-max-alleles\0max-alleles\0biallelic-only\0vcf\0bcf\0bgen\0data\0", &help_ctrl, 0,
"  --import-max-alleles <ct> : Exclude variants with more than the given # of\n"
"                              alleles during VCF/BCF/BGEN import.\n"
              );
    HelpPrint("import-overlong-var-ids\0", &help_ctrl, 0,
"  --import-overlong-var-ids <mode> :\n"
"    Specify how variants with overlong (>" MAX_ID_SLEN_STR " chars) IDs should\n"
"    be handled during import of non-PLINK formats.  Available modes:\n"
"    * 'error'/'e' (default): Error out.\n"
"    * 'missing'/'m': Keep variant, change ID to --missing-var-code string.\n"
"    * 'skip'/'s': Skip variant.\n"
"    * 'truncate'/'t': Keep variant, truncate ID to first " MAX_ID_SLEN_STR " chars.\n"
              );
    HelpPrint("read-freq\0bad-freqs\0", &help_ctrl, 0,
"  --read-freq <file> : Load allele frequency estimates from the given --freq or\n"
"                       --geno-counts (or PLINK 1.9 --freqx) report, instead of\n"
"                       imputing them from the immediate dataset.\n"
               );
// todo: something like <check-ctrls>/<check-ctrl=[case/ctrl phenotype name]>
// and maybe <ctrls-only>/<ctrl-only=[case/ctrl phenotype name]>
    HelpPrint("hwe\0", &help_ctrl, 0,
"  --hwe <p> [k] ['midp'] ['keep-fewhet'] :\n"
"    Exclude variants with Hardy-Weinberg equilibrium exact test p-values less\n"
"    than p * 10^{-nk}, where n is the sample size.\n"
"    * If unspecified, k is 0.  However, because --hwe has frequently been used\n"
"      with inappropriately strict thresholds on large datasets, this can now\n"
"      result in an error; explicitly specify k=0 to override.\n"
"    * By default, only founders are considered.\n"
"    * chrX p-values are now computed using Graffelman and Weir's method.\n"
"    * For variants with j alleles where j>2, j one-vs.-rest 'biallelic' tests\n"
"      are performed, and the variant is filtered out if any of them fail.\n"
"    * With 'keep-fewhet', variants which fail the test in the too-few-hets\n"
"      direction are not excluded.  On chrX, this uses the ratio between the\n"
"      Graffelman/Weir p-value and the female-only p-value.\n"
"    * There is currently no special handling of case/control phenotypes.\n"
              );
    HelpPrint("mach-r2-filter\0minimac3-r2-filter\0", &help_ctrl, 0,
"  --mach-r2-filter [min] [max] : Exclude variants with MaCH imputation quality\n"
"                                 metric less than min or greater than max\n"
"                                 (defaults 0.1 and 2.0).  (Monomorphic\n"
"                                 variants, with r2 = nan, are not excluded.)\n"
"                                 * This is NOT identical to the R2 metric\n"
"                                   reported by Minimac3 0.1.13+; see below.\n"
"                                 * If a single argument is provided, it is\n"
"                                   treated as the minimum.\n"
"                                 * The metric is not computed on chrX and MT.\n"
"  --minimac3-r2-filter <min> [max] : Compute Minimac3 R2 values from scratch,\n"
"                                     and exclude variants with R2 less than min\n"
"                                     or (if max is provided) greater than max.\n"
"                                     * Note that this requires phased-dosage\n"
"                                       data for all samples and variants;\n"
"                                       otherwise this will systematically\n"
"                                       underestimate imputation quality, since\n"
"                                       unphased hardcalls/dosages are treated\n"
"                                       as if they were maximally uncertain.\n"
"                                       (Use --extract-if-info/--exclude-if-info\n"
"                                       to filter on precomputed Minimac3 R2 in\n"
"                                       a VCF/.pvar INFO column.)\n"
               );
    HelpPrint("me\0me-exclude-one\0", &help_ctrl, 0,
"  --me <t> <v> ['var-first'] : Filter out trios and variants with Mendel error\n"
"                               rates exceeding the given thresholds.\n"
"  --me-exclude-one [ratio]   : Make --me exclude only one sample per trio.\n"
              );
    HelpPrint("keep-females\0keep-males\0keep-nosex\0remove-females\0remove-males\0remove-nosex\0filter-males\0filter-females\0", &help_ctrl, 0,
"  --keep-females     : Exclude male and unknown-sex samples.\n"
"  --keep-males       : Exclude female and unknown-sex samples.\n"
"  --keep-nosex       : Exclude all known-sex samples.\n"
"  --remove-females   : Exclude female samples.\n"
"  --remove-males     : Exclude male samples.\n"
"  --remove-nosex     : Exclude unknown-sex samples.\n"
               );
    HelpPrint("keep-founders\0keep-nonfounders\0filter-founders\0filter-nonfounders\0geno-counts\0", &help_ctrl, 0,
"  --keep-founders    : Exclude nonfounder samples.\n"
"  --keep-nonfounders : Exclude founder samples.\n"
               );
    // possible todo: allow or/and of multiple predicates
    // best if syntax allows for '=' character inside phenotype/covariate
    // names, though...
    HelpPrint("keep-if\0remove-if\0filter-cases\0filter-controls\0prune\0", &help_ctrl, 0,
"  --keep-if <expr...>   : Exclude samples which don't/do satisfy a boolean\n"
"  --remove-if <ex...>     expression on phenotypes/covariates, e.g.\n"
"                            --keep-if '(PHENO1 == case) || (0 < PHENO2 < 1)'\n"
"                          Unless the operator is !=, a predicate always\n"
"                          evaluates to false when the phenotype/covariate is\n"
"                          missing.\n"
               );
    HelpPrint("ac-founders\0nonfounders\0freq\0hardy\0hwe\0bad-freqs\0maf\0min-af\0max-maf\0max-af\0mac\0min-ac\0max-mac\0max-ac\0", &help_ctrl, 0,
"  --nonfounders      : Include nonfounders in allele freq/count/HWE\n"
"                       calculations.\n"
              );
    HelpPrint("ac-founders\0nonfounders\0freq\0mac\0min-ac\0max-mac\0max-ac\0", &help_ctrl, 0,
"  --ac-founders      : Confirm that nonfounders should be excluded from\n"
"                       --mac/--max-mac/\"--freq counts\".\n"
              );
    HelpPrint("make-founders\0", &help_ctrl, 0,
"  --make-founders ['require-2-missing'] ['first'] :\n"
"    Clear parental IDs for those with 1+ missing parent(s).\n"
              );
    HelpPrint("bad-freqs\0", &help_ctrl, 0,
"  --bad-freqs        : When PLINK 2 needs decent allele frequencies, it\n"
"                       normally errors out if they aren't provided by\n"
"                       --read-freq and less than 50 founders are available to\n"
"                       impute them from.  Use --bad-freqs to force PLINK 2 to\n"
"                       proceed in this case.\n"
              );
    HelpPrint("error-on-freq-calc\0read-freq\0", &help_ctrl, 0,
"  --error-on-freq-calc : When working with a very large dataset, the allele\n"
"                         frequency calculation can be expensive.\n"
"                         --error-on-freq-calc can help ensure that you aren't\n"
"                         invoking it unnecessarily.\n"
              );
    HelpPrint("bad-ld\0", &help_ctrl, 0,
"  --bad-ld             : PLINK 2 normally errors out when it needs to estimate\n"
"                         LD between variants, but there are less than 50\n"
"                         founders to estimate from.  Use --bad-ld to force\n"
"                         PLINK 2 to proceed.\n"
              );
    HelpPrint("export-allele\0recode-allele\0export\0recode", &help_ctrl, 0,
"  --export-allele <file> : With --export A/AD/Av, count alleles named in the\n"
"                           file, instead of REF alleles.\n"
              );
    HelpPrint("output-chr\0rename-chrs\0", &help_ctrl, 0,
"  --output-chr <MT code> : Set chromosome coding scheme in output files by\n"
"                           providing the desired human mitochondrial code.\n"
"                           Options are '26', 'M', 'MT', '0M', 'chr26', 'chrM',\n"
"                           and 'chrMT'; default is now 'MT' (note that this is\n"
"                           a change from PLINK 1.x, which defaulted to '26').\n"
               );
    HelpPrint("output-missing-genotype\0output-missing-phenotype\0missing-genotype\0missing-phenotype\0", &help_ctrl, 0,
"  --output-missing-genotype <ch> : Set the code used to represent missing\n"
"                                   genotypes in PLINK-format files generated by\n"
"                                   --make-[b]pgen/--make-bed/--export (default\n"
"                                   '.' unless that breaks PLINK 1.9, in which\n"
"                                   case it's '0').\n"
"  --output-missing-phenotype <s> : Set the string used to represent missing\n"
"                                   phenotypes in PLINK-format files generated\n"
"                                   by --make-[b]pgen/--make-bed/--export\n"
"                                   (default 'NA' for .psam, -9 for older).\n"
               );
    HelpPrint("sort-vars\0rename-chrs\0update-chr\0", &help_ctrl, 0,
"  --sort-vars [mode]      : Sort variants by chromosome, then position, then\n"
"                            ID.  The following string orders are supported:\n"
"                            * 'natural'/'n': Natural sort (default).\n"
"                            * 'ascii'/'a': ASCII.\n"
"                            This must be used with --pmerge[-list],\n"
"                            --make-[b]pgen/--make-bed, or\n"
"                            --make-just-{bim,pvar}.\n"
               );
    HelpPrint("zero-cluster\0", &help_ctrl, 0,
"  --zero-cluster <filename> [pheno/covar name] :\n"
"    Set blocks of genotype calls to missing.\n"
"    * The input file should have variant IDs in the first column and category\n"
"      IDs in the second.\n"
"    * If multiple categorical phenotypes are loaded, you must specify the\n"
"      phenotype to use.\n"
              );
    HelpPrint("set-invalid-haploid-missing\0set-hh-missing\0set-mixed-mt-missing\0", &help_ctrl, 0,
"  --set-invalid-haploid-missing ['keep-dosage'] :\n"
"    Make --make-[b]pgen/--make-bed set non-MT heterozygous haploid hardcalls,\n"
"    and all female chrY calls, to missing.\n"
"    By default, all associated dosages are also erased; use 'keep-dosage' to\n"
"    keep them all.\n"
"  --set-mixed-mt-missing ['keep-dosage'] : Make --make-[b]pgen/--make-bed set\n"
"                                           mixed MT hardcalls to missing.\n"
               );
    HelpPrint("set-me-missing\0", &help_ctrl, 0,
"  --set-me-missing        : Make --make-[b]pgen/--make-bed set Mendel errors\n"
"                            (as determined from hardcalls) to missing.  All\n"
"                            associated dosages are also erased.\n"
              );
    HelpPrint("fill-missing-with-ref\0fill-missing-a2\0", &help_ctrl, 0,
"  --fill-missing-with-ref : Make --make-[b]pgen/--make-bed replace all missing\n"
"                            dosages with homozygous-REF.\n"
              );
    HelpPrint("split-par\0merge-par\0split-x\0merge-x\0vcf\0bcf\0", &help_ctrl, 0,
"  --split-par <bp1> <bp2> : Changes chromosome code of all X chromosome\n"
"  --split-par <build>       variants with bp position <= bp1 to PAR1, and those\n"
"                            with position >= bp2 to PAR2.  The following build\n"
"                            codes are supported as shorthand:\n"
"                            * 'b36'/'hg18' = NCBI 36, 2709521/154584237\n"
"                            * 'b37'/'hg19' = GRCh37, 2699520/154931044\n"
"                            * 'b38'/'hg38' = GRCh38, 2781479/155701383\n"
"                            * 'chm13' = T2T-CHM13, 2394410/153925835\n"
"  --merge-par             : Merge PAR1/PAR2 back with X.  Requires PAR1 to be\n"
"                            positioned immediately before X, and PAR2 to be\n"
"                            immediately after X.  (Should *not* be used with\n"
"                            \"--export vcf\", since it causes male\n"
"                            homozygous/missing calls in PAR1/PAR2 to be\n"
"                            reported as haploid.)\n"
"  --merge-x               : Merge XY back with X.  This usually has to be\n"
"                            combined with --sort-vars.\n"
               );
    HelpPrint("lax-chrx-import\0vcf\0bcf\0gen\0bgen\0data\0haps\0", &help_ctrl, 0,
"  --lax-chrx-import       : During import of non-PLINK-format data that appears\n"
"                            to contain chrX, suppress the usual error if\n"
"                            --split-par, --impute-sex, and/or a\n"
"                            .fam/.psam/--update-sex file is expected and not\n"
"                            present.\n"
              );
    // Probably want a dosage mode, where 0/0/1 gets imported as DS=0.66667,
    // etc.
    // Do we need a mode that imports 0/1/. as DS=1?  ('partial-dosage'?
    // Presumably this would force the --vcf-half-call mode to 'haploid'.)
    HelpPrint("polyploid-mode\0vcf\0bcf\0bgen\0", &help_ctrl, 0,
"  --polyploid-mode <mode> : Specify how ploidy > 2 should be handled during\n"
"                            import.  The following two modes are supported:\n"
"                            * 'error'/'e' (default) errors out.\n"
"                            * 'missing'/'m' treats them as missing.\n"
              );
    HelpPrint("set-all-var-ids\0set-missing-var-ids\0var-id-multi\0var-id-multi-nonsnp\0new-id-max-allele-len\0", &help_ctrl, 0,
"  --set-missing-var-ids <t>  : Given a template string with a '@' where the\n"
"  --set-all-var-ids <t>        chromosome code should go and '#' where the bp\n"
"                               coordinate belongs, --set-missing-var-ids\n"
"                               assigns chromosome-and-bp-based IDs to unnamed\n"
"                               variants, while --set-all-var-ids resets all\n"
"                               IDs.\n"
"                               You may also use '$r'/'$a' to refer to the\n"
"                               ref and alt1 alleles, or '$1'/'$2' to refer to\n"
"                               them in alphabetical order.\n"
"  --var-id-multi <t>         : Specify alternative templates for multiallelic\n"
"  --var-id-multi-nonsnp <t>    variants.  ('$a' and '$1'/'$2' should be avoided\n"
"                               here, though they're technically still allowed.)\n"
"  --new-id-max-allele-len <len> [{error | missing | truncate}] :\n"
"    Specify maximum number of leading characters from allele codes to include\n"
"    in new variant IDs, and behavior on longer codes (defaults 23, error).\n"
              );
    HelpPrint("missing-var-code\0rm-dup\0set-all-var-ids\0set-missing-var-ids\0", &help_ctrl, 0,
"  --missing-var-code <str>   : Change unnamed variant code for --rm-dup,\n"
"                               --set-{missing|all}-var-ids, --recover-var-ids,\n"
"                               and --import-overlong-var-ids (default '.').\n"
               );
    HelpPrint("update-chr\0update-map\0update-name\0", &help_ctrl, 0,
"  --update-chr  <f> [chrcol] [IDcol]  [skip] : Update variant chromosome codes.\n"
"                                               Now requires --sort-vars.\n"
"  --update-map  <f> [bpcol]  [IDcol]  [skip] : Update variant bp positions.\n"
"  --update-name <f> [newcol] [oldcol] [skip] : Update variant IDs.\n"
               );
    HelpPrint("rename-chrs\0update-chr\0", &help_ctrl, 0,
"  --rename-chrs <fn> : Renames chromosomes/contigs, given a file with old names\n"
"                       in the first column and new names in the second.\n"
"                       Requires --sort-vars.\n"
"                       Note that this does not select between PLINK's built-in\n"
"                       ways of rendering ordinary chromosome codes (e.g. '23'\n"
"                       vs. 'X' vs. 'chrX'); that's what --output-chr is for.\n"
              );
    HelpPrint("recover-var-ids\0set-all-var-ids\0update-name\0", &help_ctrl, 0,
"  --recover-var-ids <file> ['strict-bim-order'] [{rigid | force}] ['partial'] :\n"
"    Undo --set-all-var-ids, given the original .pvar/VCF/.bim file.  Original\n"
"    IDs are looked up by position and allele codes.\n"
"    * By default, if the original-ID file is a .bim, allele order is ignored.\n"
"      Use 'strict-bim-order' to force A1=ALT, A2=REF.\n"
"    * If any variant has multiple matching records in the original-ID file, and\n"
"      the IDs conflict, --recover-var-ids writes the affected (current) ID(s)\n"
"      to <output prefix>.recoverid.dup, and normally errors out.  If the\n"
"      original-ID file has the same number of variants in the same order, you\n"
"      can still recover the old IDs with the 'rigid' modifier in this case.\n"
"      Alternatively, to proceed and assign the missing-ID code to these\n"
"      variants, add the 'force' modifier.  (The .recoverid.dup file is still\n"
"      written when 'rigid' or 'force' is specified.)\n"
"    * --recover-var-ids normally expects to replace all variant IDs, and errors\n"
"      out if any are left untouched.  Add the 'partial' modifier when you\n"
"      actually want to update just a proper subset.\n"
              );
    HelpPrint("update-alleles\0", &help_ctrl, 0,
"  --update-alleles ['allow-mismatch'] ['strict-missing'] <filename> :\n"
"    Update variant allele codes.\n"
"    * Input file can be 3 or 5 columns.  If 3-column, variant IDs are expected\n"
"      in the first column, comma-separated old allele codes are expected in\n"
"      column 2, and comma-separated new allele codes are expected in column 3.\n"
"      If 5-column, old allele codes are expected in columns 2-3 and new allele\n"
"      codes in columns 4-5.\n"
"    * If an entry's old alleles don't line up with the main dataset, it is\n"
"      skipped and the variant ID is logged to <output prefix>.allele.no.snp.\n"
"      The 'allow-mismatch' modifier relaxes the allele-matching requirement:\n"
"      matching alleles are updated even when mismatching allele(s) are present\n"
"      (and no .allele.no.snp entry is written when a partial update occurs).\n"
"    * By default, if an allele code in the main dataset is missing, it is\n"
"      treated as a wildcard.  'strict-missing' causes it to only match missing\n"
"      allele codes.\n"
              );
    HelpPrint("allele1234\0alleleACGT\0alleleacgt\0", &help_ctrl, 0,
"  --allele1234 ['multichar'] : Interpret/recode A/C/G/T alleles (lowercase\n"
"                               permitted) as 1/2/3/4.  With 'multichar', longer\n"
"                               allele codes are converted in the same manner.\n"
"                               Now errors out if any nonmissing allele code is\n"
"                               not fully converted.\n"
"  --alleleACGT ['multichar'] : Reverse of --allele1234.\n"
              );
    HelpPrint("update-ids\0update-parents\0update-sex\0", &help_ctrl, 0,
"  --update-ids <fname>       : Update sample IDs.\n"
"  --update-parents <fname>   : Update parental IDs.\n"
"  --update-sex <filename> ['col-num='<n>] ['male0'] :\n"
"    Update sex information.\n"
"    * By default, if there is a header line starting with '#FID'/'#IID', sex is\n"
"      loaded from the first column titled 'SEX' (any capitalization);\n"
"      otherwise, column 3 is assumed.  Use 'col-num=' to force a column number.\n"
"    * Only the first character in the sex column is processed.  By default,\n"
"      '1'/'M'/'m' is interpreted as male, '2'/'F'/'f' is interpreted as female,\n"
"      and '0'/'N'/'U'/'u' is interpreted as unknown-sex.  To change this to\n"
"      '0'/'M'/'m' = male, '1'/'F'/'f' = female, anything else other than '2' =\n"
"      unknown-sex, add 'male0'.\n"
              );
    HelpPrint("flip\0flip-subset\0", &help_ctrl, 0,
"  --flip <fn> ['permissive'] : Flip alleles (A<->T, C<->G) for SNP IDs in the\n"
"                               file.  By default, this now errors out upon\n"
"                               encountering a non-SNP; specify 'permissive' to\n"
"                               skip those variants instead.\n"
"  --flip-subset <filename>   : Only apply --flip to samples in --flip-subset\n"
"                               file.\n"
              );
    // don't make --real-ref-alleles apply to e.g. Oxford import, since
    // explicit 'ref-first'/'ref-last' modifiers are clearer
    HelpPrint("real-ref-alleles\0", &help_ctrl, 0,
"  --real-ref-alleles  : Treat A2 alleles in a PLINK 1.x fileset as actual REF\n"
"                        alleles; otherwise they're marked as provisional.\n"
               );
    HelpPrint("maj-ref\0ref-allele\0alt-allele\0alt1-allele\0a1-allele\0reference-allele\0update-ref-allele\0a2-allele\0keep-allele-order\0", &help_ctrl, 0,
"  --ref-allele ['force'] <filename> [refcol] [IDcol] [skip]\n"
"  --alt-allele ['force'] <filename> [altcol] [IDcol] [skip]\n"
"  --alt1-allele ['force'] <filename> [alt1col] [IDcol] [skip] :\n"
"    Set REF/ALT allele order.  For each input row, --ref-allele sets the given\n"
"    allele to REF, --alt1-allele sets the given allele to ALT1, and\n"
"    --alt-allele sets all ALT allele(s).\n"
"    * --ref-allele can be used with --alt[1]-allele in the same run.\n"
"    * These can only be used in runs with --make-bed/--make-[b]pgen/--export\n"
"      and no other commands.\n"
"    * \"--ref-allele <VCF filename> 4 3 '#'\", which scrapes reference allele\n"
"      assignments from a VCF file, is especially useful.\n"
"    * By default, these error out when asked to change a 'known' reference\n"
"      allele.  Add 'force' to permit that (when e.g. switching to a new\n"
"      reference genome).\n"
"    * When --alt[1]-allele moves the previous REF allele to an ALT position,\n"
"      and the new REF allele isn't explicitly set by --ref-allele, the (first)\n"
"      free ALT allele is set to REF and marked as provisional.\n"
"  --maj-ref ['force'] :\n"
"    Set major alleles to REF, like PLINK 1.x automatically did.  (Note that\n"
"    this is now opt-in rather than opt-out; --keep-allele-order is no longer\n"
"    necessary to prevent allele-swapping.)  For multiallelic variants, this\n"
"    also sorts ALT alleles by decreasing frequency, with ties going to the\n"
"    originally-earlier allele.\n"
"    * This is always based on current-dataset allele frequencies.  To reduce\n"
"      potential for confusion, --maj-ref and --read-freq are no longer allowed\n"
"      to be in the same run.\n"
"    * This can only be used in runs with --make-bed/--make-[b]pgen/--export and\n"
"      no other commands.\n"
"    * By default, this only affects variants marked as having 'provisional'\n"
"      reference alleles.  Add 'force' to apply this to all variants.\n"
"    * All new reference alleles are marked as provisional.\n"
               );
    HelpPrint("ref-from-fa\0maj-ref\0ref-allele\0reference-allele\0update-ref-allele\0a2-allele\0keep-allele-order\0fa\0", &help_ctrl, 0,
"  --ref-from-fa ['force'] : This sets reference alleles from the --fa file when\n"
"                            it can be done unambiguously (note that it's never\n"
"                            possible for deletions or some insertions).\n"
"                            By default, it errors out when asked to change a\n"
"                            'known' reference allele; add the 'force' modifier\n"
"                            to permit that.\n"
               );
    HelpPrint("normalize\0norm\0fa\0", &help_ctrl, 0,
"  --normalize ['list'] ['adjust-overlapping-deletions'] :\n"
"    (alias: --norm)\n"
"    Left-normalize all variants, using the --fa file.  (Assumes no differences\n"
"    in capitalization.)\n"
"    * 'list' causes a list of affected variant IDs to be written to\n"
"      <output prefix>.normalized.\n"
"    * 'adjust-overlapping-deletions' allows the span of '*'\n"
"      overlapping-deletion alleles to be adjusted.\n"
              );
    HelpPrint("indiv-sort\0pmerge\0pmerge-list\0", &help_ctrl, 0,
"  --indiv-sort <mode> [f] : Specify sample ID sort order for merge and\n"
"                            --make-[b]pgen/--make-bed.  The following four\n"
"                            modes are supported:\n"
"                            * 'none'/'0' keeps samples in the order they were\n"
"                              loaded.  Default for non-merge.\n"
"                            * 'natural'/'n' invokes \"natural sort\", e.g.\n"
"                              'id2' < 'ID3' < 'id10'.  Default when merging.\n"
"                            * 'ascii'/'a' sorts in ASCII order, e.g.\n"
"                              'ID3' < 'id10' < 'id2'.\n"
"                            * 'file'/'f' uses the order in the given file\n"
"                              (named in the last argument).\n"
               );
    HelpPrint("pmerge\0pmerge-list\0delete-pmerge-result\0pmerge-list-dir\0pmerge-output-vzs\0sample-inner-join\0variant-inner-join\0pheno-inner-join\0merge-mode\0merge-parents-mode\0merge-sex-mode\0merge-pheno-mode\0merge-xheader-mode\0merge-qual-mode\0merge-filter-mode\0merge-info-mode\0merge-cm-mode\0", &help_ctrl, 0,
"  --pmerge-list-dir <dir>  : Specify base dir to join to --pmerge-list entries.\n"
"  --pmerge-output-vzs      : Compress the .pvar file from --pmerge[-list].\n"
"  --delete-pmerge-result   : Delete --pmerge[-list] output files at the end of\n"
"                             the run.\n"
"  --sample-inner-join      : By default, --pmerge[-list] performs an 'outer\n"
"  --variant-inner-join       join': the merged fileset contains the union of\n"
"  --pheno-inner-join         the samples in the input filesets, and ditto for\n"
"                             variants and phenotypes.\n"
"                             --{sample,variant,pheno}-inner-join specifies an\n"
"                             intersection instead.\n"
"  --merge-mode <mode>      : Set --pmerge[-list] conflict resolution mode for\n"
"  --merge-parents-mode <m>   genotypes/dosages, parents, sexes, and phenotypes,\n"
"  --merge-sex-mode <mode>    respectively.\n"
"  --merge-pheno-mode <m>     * 'nm-match'/'1' = nonmissing values must match\n"
"                                                (default)\n"
"                             * 'nm-first'/'2' = keep first nonmissing value\n"
"                             * 'first'/'4' = keep first value, even if missing\n"
"  --merge-xheader-mode <m> : Set conflict resolution mode for .pvar header\n"
"                             entries.\n"
"                             * 'erase' = remove all\n"
"                             * 'match' = discard when there's ANY difference in\n"
"                                         the values (even capitalization)\n"
"                             * 'first' = keep first value (default)\n"
"  --merge-qual-mode <mode> : Set conflict resolution mode for\n"
"  --merge-filter-mode <m>    QUAL/FILTER/INFO/CM entries.\n"
"  --merge-info-mode <mode>   * 'erase' = remove column\n"
"  --merge-cm-mode <mode>     * 'nm-match' = nonmissing values must match\n"
"                             * 'nm-first' = keep first nonmissing (info/CM\n"
"                                            default)\n"
"                             * 'first' = keep first value, even if missing\n"
"                             * 'min' = keep minimum value (--merge-qual-mode\n"
"                                       default, not applicable to others)\n"
"                             * 'np-union' = keep all non-PASS values\n"
"                                            (--merge-filter-mode default, not\n"
"                                            applicable to others)\n"
              );
    HelpPrint("pmerge\0pmerge-list\0merge-pheno-sort\0merge-info-sort\0", &help_ctrl, 0,
"  --merge-pheno-sort <m>   : Set sort order for phenotype columns and INFO\n"
"  --merge-info-sort <mode>   entries when merging.\n"
"                             * 'none'/'0' = keep in loaded order (default)\n"
"                             * 'ascii'/'a' = ASCII order\n"
"                             * 'natural'/'n' = natural sort\n"
              );
    HelpPrint("pmerge\0pmerge-list\0merge-max-alleles\0merge-max-allele-ct\0", &help_ctrl, 0,
"  --merge-max-alleles <ct> : Exclude merged variants with more than the\n"
"                             specified number of alleles.\n"
              );
    HelpPrint("merge-sids\0pmerge\0pmerge-list\0", &help_ctrl, 0,
"  --merge-sids             : When --pmerge[-list] encounters multiple samples\n"
"                             with identical FID+IID, merge them into a single\n"
"                             sample with SID 0.\n"
              );
    HelpPrint("multiallelics-already-joined\0pmerge\0pmerge-list\0", &help_ctrl, 0,
"  --multiallelics-already-joined : Prevent --pmerge[-list] from erroring out\n"
"                                   when a .pvar file appears to have a 'split'\n"
"                                   multiallelic variant.\n"
              );
    HelpPrint("mendel-duos\0mendel-missing-in-denom\0me\0mendel\0set-me-missing\0", &help_ctrl, 0,
"  --mendel-duos             : Make Mendel error checks consider samples with\n"
"                              only one parent in the dataset.\n"
"  --mendel-missing-in-denom : When the child has a missing genotype, or both\n"
"                              parents have missing genotypes, don't exclude the\n"
"                              observation from error rate denominators.\n"
              );
    HelpPrint("indep-preferred\0indep-pairwise\0", &help_ctrl, 0,
"  --indep-preferred <filename>   : Make LD-pruning commands try to keep the\n"
"                                   variants listed in a file.\n"
              );
    HelpPrint("indep-order\0indep-pairwise\0", &help_ctrl, 0,
"  --indep-order <mode> : Set LD-pruning order.\n"
"                         * '1' = replicate PLINK 1.x\n"
"                         * '2' = within each window, scan backwards (default)\n"
              );
    HelpPrint("ld-window\0ld-window-kb\0ld-window-cm\0ld-window-r2\0r-phased\0r-unphased\0r2-phased\0r2-unphased\0r\0r2\0", &help_ctrl, 0,
"  --ld-window <#var+1> : Limit --r[2]-[un]phased variant-ct distance.\n"
"  --ld-window-kb <#kb> : Change tabular --r[2]-[un]phased max kb distance\n"
"                         (default 1000).\n"
"  --ld-window-cm <#cm> : Limit --r[2]-[un]phased centimorgan distance.\n"
              );
    HelpPrint("ld-window-r2\0r-phased\0r-unphased\0r2-phased\0r2-unphased\0r\0r2\0", &help_ctrl, 0,
"  --ld-window-r2 <min> : Change tabular --r[2]-[un]phased minimum r^2 (default\n"
"                         0.2).\n"
              );
    HelpPrint("ld-snp\0ld-snps\0ld-snp-list\0r-phased\0r-unphased\0r2-phased\0r2-unphased\0r\0r2\0", &help_ctrl, 0,
"  --ld-snp <var. ID>   : Restrict the first variant in --r[2]-[un]phased\n"
"  --ld-snps <varID...>   variant-pairs to a limited set.  --ld-snp specifies\n"
"  --ld-snp-list <file>   a single ID, --ld-snps accepts one or more ranges\n"
"                         (same syntax as --snps), and --ld-snp-list specifies a\n"
"                         file to load variant IDs from.\n"
              );
    // todo: add citation for 2018 KING update paper, which should discuss the
    // two-stage screen + refine workflow supported by --king-table-subset,
    // when it comes out
    HelpPrint("make-king\0make-king-table\0king-table-filter\0king-table-subset\0king-table-require\0king-table-require-xor\0", &help_ctrl, 0,
"  --king-table-filter <min>      : Specify minimum kinship coefficient for\n"
"                                   inclusion in --make-king-table report.\n"
"  --king-table-subset <f> [kmin] : Restrict current --make-king-table run to\n"
"                                   sample pairs listed in the given .kin0 file.\n"
"                                   If a second argument is provided, only\n"
"                                   sample pairs with kinship >= that threshold\n"
"                                   (in the input .kin0) are processed.\n"
"  --king-table-require <fn...>   : Restrict current --make-king-table run to\n"
"                                   sample pairs that include at least one of\n"
"                                   the samples in the given file.\n"
"  --king-table-require-xor <...> : Restrict current --make-king-table run to\n"
"                                   sample pairs that include exactly one of the\n"
"                                   samples in the given file.\n"
               );
    HelpPrint("glm\0linear\0logistic\0condition\0condition-list\0parameters\0tests\0", &help_ctrl, 0,
"  --condition <variant ID> [{dominant | recessive}] ['multiallelic']\n"
"  --condition-list <fname> [{dominant | recessive}] ['multiallelic'] :\n"
"    Add the given variant, or all variants in the given file, as --glm\n"
"    covariates.\n"
"    By default, this errors out if any of the variants are multiallelic; add\n"
"    the 'multiallelic' ('m' for short) modifier to allow them.  They'll\n"
"    effectively be split against the major allele (unless --glm's 'omit-ref'\n"
"    modifier was specified), and all induced covariate names--even for\n"
"    biallelic variants--will have an underscore followed by the allele code at\n"
"    the end.\n"
"  --parameters <...> : Include only the given covariates/interactions in the\n"
"                       --glm model, identified by a list of 1-based indices\n"
"                       and/or ranges of them.\n"
"  --tests <...>      : Perform a (joint) test on the specified term(s) in the\n"
"  --tests all          --glm model, identified by 1-based indices and/or ranges\n"
"                       of them.\n"
              /*
"                       of them.  If permutation was requested, it is based on\n"
"                       this test.\n"
              */
"                       * Note that, when --parameters is also present, the\n"
"                         indices refer to the terms remaining AFTER pruning by\n"
"                         --parameters.\n"
"                       * You can use '--tests all' to include all terms.\n"
               );
    HelpPrint("glm\0linear\0logistic\0vif\0max-corr\0", &help_ctrl, 0,
"  --vif <max VIF>    : Set VIF threshold for --glm multicollinearity check\n"
"                       (default 50).  (This is no longer skipped for\n"
"                       case/control phenotypes.)\n"
"  --max-corr <val>   : Skip --glm regression when the absolute value of the\n"
"                       correlation between two predictors exceeds this value\n"
"                       (default 0.999).\n"
               );
    HelpPrint("xchr-model\0glm\0linear\0logistic\0score\0score-list\0vscore\0", &help_ctrl, 0,
"  --xchr-model <m>   : Set the chrX model for --glm, --condition[-list],\n"
"                       --score[-list], and --vscore.\n"
"                       * '0' = skip chrX.\n"
"                       * '1' = add sex as a covar on chrX, code males 0..1.\n"
"                       * '2' (default) = chrX sex covar, code males 0..2.\n"
"                       (Use the --glm 'interaction' modifier to test for\n"
"                       interaction between genotype and sex.)\n"
               );
    HelpPrint("adjust\0", &help_ctrl, 0,
"  --adjust ['zs'] ['gc'] ['log10'] ['cols='<column set descriptor>] :\n"
"    For each association test in this run, report some basic multiple-testing\n"
"    corrections, sorted in increasing-p-value order.  Modifiers work the same\n"
"    way as they do on --adjust-file.\n"
               );
    HelpPrint("adjust\0adjust-file\0lambda\0", &help_ctrl, 0,
"  --lambda           : Set genomic control lambda for --adjust[-file].\n"
               );
    HelpPrint("adjust-chr-field\0adjust-pos-field\0adjust-id-field\0adjust-ref-field\0adjust-alt-field\0adjust-a1-field\0adjust-test-field\0adjust-p-field\0adjust-file\0", &help_ctrl, 0,
"  --adjust-chr-field <n...>     : Set --adjust-file input field names.  When\n"
"  --adjust-pos-field <n...>       multiple arguments are given to these flags,\n"
"  --adjust-id-field <n...>        earlier names take precedence over later\n"
"  --adjust-ref-field <n...>       ones.\n"
"  --adjust-alt-field <n...>\n"
"  --adjust-provref-field <n...>\n"
"  --adjust-a1-field <n...>\n"
"  --adjust-test-field <n...>\n"
"  --adjust-p-field <n...>\n"
               );
    HelpPrint("ci\0linear\0logistic\0", &help_ctrl, 0,
"  --ci <size>        : Report confidence ratios for odds ratios/betas.\n"
               );
    HelpPrint("pfilter\0", &help_ctrl, 0,
"  --pfilter <val>    : Filter out assoc. test results with higher p-values.\n"
               );
    HelpPrint("permute-within\0within\0", &help_ctrl, 0,
"  --permute-within [cat. pheno/covar name] : Restrict permutation to clusters.\n"
              );
    HelpPrint("aperm\0", &help_ctrl, 0,
"  --aperm <min perms - 1> [max perms] [alpha] [beta] [init interval] [slope] :\n"
"    Set up to six parameters controlling adaptive permutation tests.\n"
"    * The first two control the minimum and maximum number of permutations that\n"
"      may be run for each variant; default values are 5 and 1000000.\n"
"    * The next two control the early termination condition.  A\n"
"      100% * (1 - beta/2T) confidence interval is calculated for each empirical\n"
"      p-value, where T is the total number of variants; whenever this\n"
"      confidence interval doesn't contain alpha, the variant is exempted from\n"
"      further permutation testing.  Default values are 0 and 1e-4.\n"
"    * The last two control when the early termination condition is checked.  If\n"
"      a check occurs at permutation #p, the next check occurs after\n"
"      [slope]p + [init interval] more permutations (rounded down).  Default\n"
"      initial interval is 1, and default slope is 0.001.\n"
               );
    HelpPrint("mperm-save\0mperm-save-all\0", &help_ctrl, 0,
"  --mperm-save       : Save best max(T) permutation test statistics.\n"
"  --mperm-save-all   : Save all max(T) permutation test statistics.\n"
               );
    HelpPrint("clump-p1\0clump-p2\0clump-r2\0clump-kb\0clump-unphased\0clump-log10\0clump-range\0clump-range0\0clump-range-border\0clump-bins\0clump-id-field\0clump-p-field\0clump-a1-field\0clump-test-field\0clump-force-a1\0clump-test\0clump-snp-field\0clump-field\0clump\0", &help_ctrl, 0,
"  --clump-p1 <pval> : Set --clump index var. p-value ceiling (default 1e-4).\n"
"  --clump-p2 <pval> : Set --clump secondary p-value threshold (default 0.01).\n"
"  --clump-r2 <r^2>  : Set --clump r^2 threshold (default 0.5).\n"
"  --clump-kb <# kb> : Set --clump kb radius (default 250).\n"
"  --clump-unphased  : Make --clump use unphased rather than phased r^2.\n"
"  --clump-log10 ['input-only' | 'output-only'] : Read and/or write p-values in\n"
"                                                 -log10 form.\n"
"  --clump-log10-p1 <-l10(p)> : Alternatives to --clump-p1/--clump-p2 that take\n"
"  --clump-log10-p2 <-l10(p)>   the p-value argument in -log10 form.\n"
"  --clump-range[0] <fname>   : Report overlaps between clumps and regions.\n"
"                               --clump-range0 specifies 0-based input\n"
"                               coordinates.\n"
"  --clump-range-border <kb>  : Stretch regions in --clump-range[0] file.\n"
"  --clump-bins <bndries...>  : Set --clump p-value bin boundaries (default\n"
"                               0.0001,0.001,0.01,0.05).\n"
"  --clump-id-field <nm...>   : Set --clump variant ID (default 'ID SNP'),\n"
"  --clump-p-field <nm...>      p-value (default 'P', unless -log10), effect\n"
"  --clump-a1-field [nm...]     allele (default 'A1'), and/or test (default\n"
"  --clump-test-field [n...]    'TEST') field name search orders.\n"
"                               With multiple field names, earlier names take\n"
"                               precedence over later ones.\n"
"  --clump-force-a1           : Force A1 alleles to be included in --clump\n"
"                               report for biallelic variants.\n"
"  --clump-test [test ID...]  : When the --clump-test-field column exists, only\n"
"                               consider these test value(s) (default 'ADD').\n"
              );
    HelpPrint("clump-allow-overlap\0clump\0", &help_ctrl, 0,
"  --clump-allow-overlap      : Let --clump non-index variants join multiple\n"
"                               clumps.\n"
              );
    HelpPrint("score-col-nums\0score\0score-list\0", &help_ctrl, 0,
"  --score-col-nums <...> : Process all the specified coefficient columns in the\n"
"                           --score[-list] file(s), identified by 1-based\n"
"                           indexes and/or ranges of them.\n"
               );
    HelpPrint("q-score-range\0score\0score-list\0", &help_ctrl, 0,
"  --q-score-range <range file> <data file> [i] [j] ['header'] ['min'] :\n"
"    Apply --score[-list] to subset(s) of variants in the primary score list(s)\n"
"    based on e.g. p-value ranges.\n"
"    * The first file should have range labels in the first column, p-value\n"
"      lower bounds in the second column, and upper bounds in the third column.\n"
"      Lines with too few entries, or nonnumeric values in the second or third\n"
"      column, are ignored.\n"
"    * The second file should contain a variant ID and a p-value on each line\n"
"      (except possibly the first).  Variant IDs are read from column #i and\n"
"      p-values are read from column #j, where i defaults to 1 and j defaults to\n"
"      i+1.  The 'header' modifier causes the first nonempty line of this file\n"
"      to be skipped.\n"
"    * By default, --q-score-range errors out when a variant ID appears multiple\n"
"      times in the data file (and is also present in the main dataset).  To use\n"
"      the minimum p-value in this case instead, add the 'min' modifier.\n"
               );
    HelpPrint("vscore-col-nums\0variant-score\0vscore\0", &help_ctrl, 0,
"  --vscore-col-nums <...> : Process all the specified coefficient columns in\n"
"                            the --variant-score file, identified by 1-based\n"
"                            indexes and/or ranges of them.\n"
               );
    HelpPrint("parallel\0", &help_ctrl, 0,
"  --parallel <k> <n> : Divide the output matrix into n pieces, and only compute\n"
"                       the kth piece.  The primary output file will have the\n"
"                       piece number included in its name, e.g. plink2.king.13\n"
"                       or plink2.king.13.zst if k is 13.  Concatenating these\n"
"                       files in order will yield the full matrix of interest.\n"
"                       (Yes, this can be done before decompression.)\n"
"                       N.B. This generally cannot be used to directly write a\n"
"                       symmetric square matrix.  Choose square0 or triangle\n"
"                       shape instead, and postprocess as necessary.\n"
               );
    HelpPrint("memory\0seed\0", &help_ctrl, 0,
"  --memory <val> ['require'] : Set size, in MiB, of initial workspace malloc\n"
"                               attempt.  To error out instead of reducing the\n"
"                               request size when the initial attempt fails, add\n"
"                               the 'require' modifier.\n"
               );
    HelpPrint("threads\0num_threads\0thread-num\0seed\0", &help_ctrl, 0,
"  --threads <val>    : Set maximum number of compute threads.\n"
               );
    HelpPrint("d\0covar-name\0exclude-snps\0pheno-name\0snps", &help_ctrl, 0,
"  --d <char>         : Change variant/covariate range delimiter (normally '-').\n"
              );
    HelpPrint("seed\0", &help_ctrl, 0,
"  --seed <val...>    : Set random number seed(s).  Each value must be an\n"
"                       integer between 0 and 4294967295 inclusive.\n"
"                       Note that --threads and \"--memory require\" may also be\n"
"                       needed to reproduce some randomized runs.\n"
               );
    HelpPrint("native\0", &help_ctrl, 0,
"  --native           : Allow Intel MKL to use processor-dependent code paths.\n"
              );
    HelpPrint("output-min-p\0", &help_ctrl, 0,
"  --output-min-p <p> : Specify minimum non-empirical p-value to write to\n"
"                       reports.  (2.23e-308 is useful for preventing underflow\n"
"                       in some programs.)\n"
               );
    HelpPrint("debug\0randmem\0", &help_ctrl, 0,
"  --debug            : Use slower, more crash-resistant logging method.\n"
"  --randmem          : Randomize initial workspace memory (helps catch\n"
"                       uninitialized-memory bugs).\n"
               );
    HelpPrint("warning-errcode\0", &help_ctrl, 0,
"  --warning-errcode  : Return a nonzero error code to the OS when a run\n"
"                       completes with warning(s).\n"
               );
    // possible todo: --zst-block {block size} to generate seekable files
    HelpPrint("zst-level\0", &help_ctrl, 0,
"  --zst-level <lvl>  : Set the Zstd compression level (1-22, default 3).\n"
               );
    HelpPrint("allow-misleading-out-arg\0out\0", &help_ctrl, 0,
"  --allow-misleading-out-arg   : Allow --out argument to end in a common\n"
"                                 filename extension, even though that usually\n"
"                                 corresponds to a misunderstanding of how --out\n"
"                                 works.\n"
              );
    HelpPrint("allow-normalize-with-split\0normalize\0", &help_ctrl, 0,
"  --allow-normalize-with-split : Disable the --normalize + variant-split\n"
"                                 order-of-operations warning (which will become\n"
"                                 an error in a future build).\n"
              );
    if (!param_ct) {
      fputs(
"\nPrimary methods paper:\n"
"Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015)\n"
"Second-generation PLINK: rising to the challenge of larger and richer datasets.\n"
"GigaScience, 4.\n"
, stdout);
    }
  } while (help_ctrl.iters_left--);
  if (help_ctrl.unmatched_ct) {
    net_unmatched_ct = help_ctrl.unmatched_ct;
    printf("\nNo help entr%s for", (help_ctrl.unmatched_ct == 1)? "y" : "ies");
    col_num = (help_ctrl.unmatched_ct == 1)? 17 : 19;
    arg_uidx = 0;
    // er, should replace the \n logic with a WordWrap() call
    while (help_ctrl.unmatched_ct) {
      arg_uidx = AdvTo0Bit(help_ctrl.all_match_arr, arg_uidx);
      help_ctrl.unmatched_ct--;
      if (help_ctrl.unmatched_ct) {
        if (net_unmatched_ct == 2) {
          if (help_ctrl.param_slens[arg_uidx] + col_num > 76) {
            putc_unlocked('\n', stdout);
            col_num = 2 + help_ctrl.param_slens[arg_uidx];
          } else {
            putc_unlocked(' ', stdout);
            col_num += 3 + help_ctrl.param_slens[arg_uidx];
          }
          putc_unlocked('\'', stdout);
          fputs(argvk[arg_uidx], stdout);
          putc_unlocked('\'', stdout);
        } else {
          if (help_ctrl.param_slens[arg_uidx] + col_num > 75) {
            putc_unlocked('\n', stdout);
            col_num = 3 + help_ctrl.param_slens[arg_uidx];
          } else {
            putc_unlocked(' ', stdout);
            col_num += 4 + help_ctrl.param_slens[arg_uidx];
          }
          putc_unlocked('\'', stdout);
          fputs(argvk[arg_uidx], stdout);
          fputs("',", stdout);
        }
        if (help_ctrl.unmatched_ct == 1) {
          if (col_num > 76) {
            fputs("\nor", stdout);
            col_num = 2;
          } else {
            fputs(" or", stdout);
            col_num += 3;
          }
        }
      } else {
        putc_unlocked((help_ctrl.param_slens[arg_uidx] + col_num > 75)? '\n' : ' ', stdout);
        putc_unlocked('\'', stdout);
        fputs(argvk[arg_uidx], stdout);
        fputs("\'.\n", stdout);
      }
      arg_uidx++;
    }
  }
  if (param_ct) {
    while (0) {
    DispHelp_ret_NOMEM:
      reterr = kPglRetNomem;
    }
    free_cond(help_ctrl.param_slens);
    free_cond(help_ctrl.all_match_arr);
    free_cond(new_argv);
  }
  return reterr;
}

#ifdef __cplusplus
}
#endif
