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|
#include "Parameters.h"
#include <smithwaterman/convert.h>
using namespace std;
void Parameters::simpleUsage(char ** argv) {
cout
<< "usage: " << argv[0] << " -f [REFERENCE] [OPTIONS] [BAM FILES] >[OUTPUT]" << endl
<< endl
<< "Bayesian haplotype-based polymorphism discovery." << endl
<< endl
<< "parameters:" << endl
<< endl
<< " -h --help For a complete description of options." << endl
<< endl
<< "freebayes is maintained by Erik Garrison and Pjotr Prins." << endl
<< endl
<< "citation: Erik Garrison, Gabor Marth" << endl
<< " \"Haplotype-based variant detection from short-read sequencing\"" << endl
<< " arXiv:1207.3907 (http://arxiv.org/abs/1207.3907)" << endl
<< endl
<< "author: Erik Garrison <erik.garrison@gmail.com>" << endl
<< "version: " << VERSION_GIT << endl;
}
void Parameters::usage(char** argv) {
simpleUsage(argv);
cout
<< endl
<< "overview:" << endl
<< endl
<< " To call variants from aligned short-read sequencing data, supply BAM files and" << endl
<< " a reference. FreeBayes will provide VCF output on standard out describing SNPs," << endl
<< " indels, and complex variants in samples in the input alignments." << endl
<< endl
<< " By default, FreeBayes will consider variants supported by at least 2" << endl
<< " observations in a single sample (-C) and also by at least 20% of the reads from" << endl
<< " a single sample (-F). These settings are suitable to low to high depth" << endl
<< " sequencing in haploid and diploid samples, but users working with polyploid or" << endl
<< " pooled samples may wish to adjust them depending on the characteristics of" << endl
<< " their sequencing data." << endl
<< endl
<< " FreeBayes is capable of calling variant haplotypes shorter than a read length" << endl
<< " where multiple polymorphisms segregate on the same read. The maximum distance" << endl
<< " between polymorphisms phased in this way is determined by the" << endl
<< " --max-complex-gap, which defaults to 3bp. In practice, this can comfortably be" << endl
<< " set to half the read length." << endl
<< endl
<< " Ploidy may be set to any level (-p), but by default all samples are assumed to" << endl
<< " be diploid. FreeBayes can model per-sample and per-region variation in" << endl
<< " copy-number (-A) using a copy-number variation map." << endl
<< endl
<< " FreeBayes can act as a frequency-based pooled caller and describe variants" << endl
<< " and haplotypes in terms of observation frequency rather than called genotypes." << endl
<< " To do so, use --pooled-continuous and set input filters to a suitable level." << endl
<< " Allele observation counts will be described by AO and RO fields in the VCF output." << endl
<< endl
<< endl
<< "examples:" << endl
<< endl
<< " # call variants assuming a diploid sample" << endl
<< " freebayes -f ref.fa aln.bam >var.vcf" << endl
<< endl
<< " # call variants assuming a diploid sample, providing gVCF output" << endl
<< " freebayes -f ref.fa --gvcf aln.bam >var.gvcf" << endl
<< endl
<< " # require at least 5 supporting observations to consider a variant" << endl
<< " freebayes -f ref.fa -C 5 aln.bam >var.vcf" << endl
<< endl
<< " # discard alignments overlapping positions where total read depth is greater than 200" << endl
<< " freebayes -f ref.fa -g 200 aln.bam >var.vcf" << endl
<< endl
<< " # use a different ploidy" << endl
<< " freebayes -f ref.fa -p 4 aln.bam >var.vcf" << endl
<< endl
<< " # assume a pooled sample with a known number of genome copies" << endl
<< " freebayes -f ref.fa -p 20 --pooled-discrete aln.bam >var.vcf" << endl
<< endl
<< " # generate frequency-based calls for all variants passing input thresholds" << endl
<< " freebayes -f ref.fa -F 0.01 -C 1 --pooled-continuous aln.bam >var.vcf" << endl
<< endl
<< " # use an input VCF (bgzipped + tabix indexed) to force calls at particular alleles" << endl
<< " freebayes -f ref.fa -@ in.vcf.gz aln.bam >var.vcf" << endl
<< endl
<< " # generate long haplotype calls over known variants" << endl
<< " freebayes -f ref.fa --haplotype-basis-alleles in.vcf.gz \\ " << endl
<< " --haplotype-length 50 aln.bam" << endl
<< endl
<< " # naive variant calling: simply annotate observation counts of SNPs and indels" << endl
<< " freebayes -f ref.fa --haplotype-length 0 --min-alternate-count 1 \\ " << endl
<< " --min-alternate-fraction 0 --pooled-continuous --report-monomorphic aln.bam >var.vcf" << endl
<< endl
<< endl
<< "parameters:" << endl
<< endl
<< " -h --help Prints this help dialog." << endl
<< " --version Prints the release number and the git commit id." << endl
<< endl
<< "input:" << endl
<< endl
<< " -b --bam FILE Add FILE to the set of BAM files to be analyzed." << endl
<< " -L --bam-list FILE" << endl
<< " A file containing a list of BAM files to be analyzed." << endl
<< " -c --stdin Read BAM input on stdin." << endl
<< " -f --fasta-reference FILE" << endl
<< " Use FILE as the reference sequence for analysis." << endl
<< " An index file (FILE.fai) will be created if none exists." << endl
<< " If neither --targets nor --region are specified, FreeBayes" << endl
<< " will analyze every position in this reference." << endl
<< " -t --targets FILE" << endl
<< " Limit analysis to targets listed in the BED-format FILE." << endl
<< " -r --region <chrom>:<start_position>-<end_position>" << endl
<< " Limit analysis to the specified region, 0-base coordinates," << endl
<< " end_position not included (same as BED format)." << endl
<< " Either '-' or '..' maybe used as a separator." << endl
<< " -s --samples FILE" << endl
<< " Limit analysis to samples listed (one per line) in the FILE." << endl
<< " By default FreeBayes will analyze all samples in its input" << endl
<< " BAM files." << endl
<< " --populations FILE" << endl
<< " Each line of FILE should list a sample and a population which" << endl
<< " it is part of. The population-based bayesian inference model" << endl
<< " will then be partitioned on the basis of the populations." << endl
<< " -A --cnv-map FILE" << endl
<< " Read a copy number map from the BED file FILE, which has" << endl
<< " either a sample-level ploidy:" << endl
<< " sample_name copy_number" << endl
<< " or a region-specific format:" << endl
<< " seq_name start end sample_name copy_number" << endl
<< " ... for each region in each sample which does not have the" << endl
<< " default copy number as set by --ploidy. These fields can be delimited" << endl
<< " by space or tab." << endl
<< endl
<< "output:" << endl
<< endl
<< " -v --vcf FILE Output VCF-format results to FILE. (default: stdout)" << endl
<< " --gvcf" << endl
<< " Write gVCF output, which indicates coverage in uncalled regions." << endl
<< " --gvcf-chunk NUM" << endl
<< " When writing gVCF output emit a record for every NUM bases." << endl
<< " -& --gvcf-dont-use-chunk BOOL " << endl
<< " When writing the gVCF output emit a record for all bases if" << endl
<< " set to \"true\" , will also route an int to --gvcf-chunk" << endl
<< " similar to --output-mode EMIT_ALL_SITES from GATK" << endl
<< " -@ --variant-input VCF" << endl
<< " Use variants reported in VCF file as input to the algorithm." << endl
<< " Variants in this file will included in the output even if" << endl
<< " there is not enough support in the data to pass input filters." << endl
<< " -l --only-use-input-alleles" << endl
<< " Only provide variant calls and genotype likelihoods for sites" << endl
<< " and alleles which are provided in the VCF input, and provide" << endl
<< " output in the VCF for all input alleles, not just those which" << endl
<< " have support in the data." << endl
<< " --haplotype-basis-alleles VCF" << endl
<< " When specified, only variant alleles provided in this input" << endl
<< " VCF will be used for the construction of complex or haplotype" << endl
<< " alleles." << endl
<< " --report-all-haplotype-alleles" << endl
<< " At sites where genotypes are made over haplotype alleles," << endl
<< " provide information about all alleles in output, not only" << endl
<< " those which are called." << endl
<< " --report-monomorphic" << endl
<< " Report even loci which appear to be monomorphic, and report all" << endl
<< " considered alleles, even those which are not in called genotypes." << endl
<< " Loci which do not have any potential alternates have '.' for ALT." << endl
<< " -P --pvar N Report sites if the probability that there is a polymorphism" << endl
<< " at the site is greater than N. default: 0.0. Note that post-" << endl
<< " filtering is generally recommended over the use of this parameter." << endl
<< " --strict-vcf" << endl
<< " Generate strict VCF format (FORMAT/GQ will be an int)" << endl
<< endl
<< "population model:" << endl
<< endl
<< " -T --theta N The expected mutation rate or pairwise nucleotide diversity" << endl
<< " among the population under analysis. This serves as the" << endl
<< " single parameter to the Ewens Sampling Formula prior model" << endl
<< " default: 0.001" << endl
<< " -p --ploidy N Sets the default ploidy for the analysis to N. default: 2" << endl
<< " -J --pooled-discrete" << endl
<< " Assume that samples result from pooled sequencing." << endl
<< " Model pooled samples using discrete genotypes across pools." << endl
<< " When using this flag, set --ploidy to the number of" << endl
<< " alleles in each sample or use the --cnv-map to define" << endl
<< " per-sample ploidy." << endl
<< " -K --pooled-continuous" << endl
<< " Output all alleles which pass input filters, regardles of" << endl
<< " genotyping outcome or model." << endl
<< endl
<< "reference allele:" << endl
<< endl
<< " -Z --use-reference-allele" << endl
<< " This flag includes the reference allele in the analysis as" << endl
<< " if it is another sample from the same population." << endl
<< " --reference-quality MQ,BQ" << endl
<< " Assign mapping quality of MQ to the reference allele at each" << endl
<< " site and base quality of BQ. default: 100,60" << endl
<< endl
<< "allele scope:" << endl
<< endl
<< " -n --use-best-n-alleles N" << endl
<< " Evaluate only the best N SNP alleles, ranked by sum of" << endl
<< " supporting quality scores. (Set to 0 to use all; default: all)" << endl
<< " -E --max-complex-gap N" << endl
<< " --haplotype-length N" << endl
<< " Allow haplotype calls with contiguous embedded matches of up" << endl
<< " to this length. Set N=-1 to disable clumping. (default: 3)" << endl
<< " --min-repeat-size N" << endl
<< " When assembling observations across repeats, require the total repeat" << endl
<< " length at least this many bp. (default: 5)" << endl
<< " --min-repeat-entropy N" << endl
<< " To detect interrupted repeats, build across sequence until it has" << endl
<< " entropy > N bits per bp. Set to 0 to turn off. (default: 1)" << endl
<< " --no-partial-observations" << endl
<< " Exclude observations which do not fully span the dynamically-determined" << endl
<< " detection window. (default, use all observations, dividing partial" << endl
<< " support across matching haplotypes when generating haplotypes.)" << endl
<< endl
<< " These flags are meant for testing." << endl
<< " They are not meant for filtering the output." << endl
<< " They actually filter the input to the algorithm by throwing away alignments." << endl
<< " This hurts performance by hiding information from the Bayesian model." << endl
<< " Do not use them unless you can validate that they improve results!" << endl
<< endl
<< " -I --throw-away-snp-obs Remove SNP observations from input." << endl
<< " -i --throw-away-indels-obs Remove indel observations from input." << endl
<< " -X --throw-away-mnp-obs Remove MNP observations from input." << endl
<< " -u --throw-away-complex-obs Remove complex allele observations from input." << endl
<< endl
<< " If you need to break apart haplotype calls to obtain one class of alleles," << endl
<< " run the call with default parameters, then normalize and subset the VCF:" << endl
<< " freebayes ... | vcfallelicprimitives -kg >calls.vcf" << endl
<< " For example, this would retain only biallelic SNPs." << endl
<< " <calls.vcf vcfsnps | vcfbiallelic >biallelic_snp_calls.vcf" << endl
<< endl
<< "indel realignment:" << endl
<< endl
<< " -O --dont-left-align-indels" << endl
<< " Turn off left-alignment of indels, which is enabled by default." << endl
<< endl
<< "input filters:" << endl
<< endl
<< " -4 --use-duplicate-reads" << endl
<< " Include duplicate-marked alignments in the analysis." << endl
<< " default: exclude duplicates marked as such in alignments" << endl
<< " -m --min-mapping-quality Q" << endl
<< " Exclude alignments from analysis if they have a mapping" << endl
<< " quality less than Q. default: 1" << endl
<< " -q --min-base-quality Q" << endl
<< " Exclude alleles from analysis if their supporting base" << endl
<< " quality is less than Q. default: 0" << endl
<< " -R --min-supporting-allele-qsum Q" << endl
<< " Consider any allele in which the sum of qualities of supporting" << endl
<< " observations is at least Q. default: 0" << endl
<< " -Y --min-supporting-mapping-qsum Q" << endl
<< " Consider any allele in which and the sum of mapping qualities of" << endl
<< " supporting reads is at least Q. default: 0" << endl
<< " -Q --mismatch-base-quality-threshold Q" << endl
<< " Count mismatches toward --read-mismatch-limit if the base" << endl
<< " quality of the mismatch is >= Q. default: 10" << endl
<< " -U --read-mismatch-limit N" << endl
<< " Exclude reads with more than N mismatches where each mismatch" << endl
<< " has base quality >= mismatch-base-quality-threshold." << endl
<< " default: ~unbounded" << endl
<< " -z --read-max-mismatch-fraction N" << endl
<< " Exclude reads with more than N [0,1] fraction of mismatches where" << endl
<< " each mismatch has base quality >= mismatch-base-quality-threshold" << endl
<< " default: 1.0" << endl
<< " -$ --read-snp-limit N" << endl
<< " Exclude reads with more than N base mismatches, ignoring gaps" << endl
<< " with quality >= mismatch-base-quality-threshold." << endl
<< " default: ~unbounded" << endl
<< " -e --read-indel-limit N" << endl
<< " Exclude reads with more than N separate gaps." << endl
<< " default: ~unbounded" << endl
<< " -0 --standard-filters Use stringent input base and mapping quality filters" << endl
<< " Equivalent to -m 30 -q 20 -R 0 -S 0" << endl
<< " -F --min-alternate-fraction N" << endl
<< " Require at least this fraction of observations supporting" << endl
<< " an alternate allele within a single individual in the" << endl
<< " in order to evaluate the position. default: 0.05" << endl
<< " -C --min-alternate-count N" << endl
<< " Require at least this count of observations supporting" << endl
<< " an alternate allele within a single individual in order" << endl
<< " to evaluate the position. default: 2" << endl
<< " -3 --min-alternate-qsum N" << endl
<< " Require at least this sum of quality of observations supporting" << endl
<< " an alternate allele within a single individual in order" << endl
<< " to evaluate the position. default: 0" << endl
<< " -G --min-alternate-total N" << endl
<< " Require at least this count of observations supporting" << endl
<< " an alternate allele within the total population in order" << endl
<< " to use the allele in analysis. default: 1" << endl
<< " --min-coverage N" << endl
<< " Require at least this coverage to process a site. default: 0" << endl
<< " --limit-coverage N" << endl
<< " Downsample per-sample coverage to this level if greater than this coverage." << endl
<< " default: no limit" << endl
<< " -g --skip-coverage N" << endl
<< " Skip processing of alignments overlapping positions with coverage >N." << endl
<< " This filters sites above this coverage, but will also reduce data nearby." << endl
<< " default: no limit" << endl
<< " --trim-complex-tail" << endl
<< " Trim complex tails." << endl
<< endl
<< "population priors:" << endl
<< endl
<< " -k --no-population-priors" << endl
<< " Equivalent to --pooled-discrete --hwe-priors-off and removal of" << endl
<< " Ewens Sampling Formula component of priors." << endl
<< endl
<< "mappability priors:" << endl
<< endl
<< " -w --hwe-priors-off" << endl
<< " Disable estimation of the probability of the combination" << endl
<< " arising under HWE given the allele frequency as estimated" << endl
<< " by observation frequency." << endl
<< " -V --binomial-obs-priors-off" << endl
<< " Disable incorporation of prior expectations about observations." << endl
<< " Uses read placement probability, strand balance probability," << endl
<< " and read position (5'-3') probability." << endl
<< " -a --allele-balance-priors-off" << endl
<< " Disable use of aggregate probability of observation balance between alleles" << endl
<< " as a component of the priors." << endl
<< endl
<< "genotype likelihoods:" << endl
<< endl
<< " --observation-bias FILE" << endl
<< " Read length-dependent allele observation biases from FILE." << endl
<< " The format is [length] [alignment efficiency relative to reference]" << endl
<< " where the efficiency is 1 if there is no relative observation bias." << endl
<< " --base-quality-cap Q" << endl
<< " Limit estimated observation quality by capping base quality at Q." << endl
<< " --prob-contamination F" << endl
<< " An estimate of contamination to use for all samples. default: 10e-9" << endl
<< " --legacy-gls Use legacy (polybayes equivalent) genotype likelihood calculations" << endl
<< " --contamination-estimates FILE" << endl
<< " A file containing per-sample estimates of contamination, such as" << endl
<< " those generated by VerifyBamID. The format should be:" << endl
<< " sample p(read=R|genotype=AR) p(read=A|genotype=AA)" << endl
<< " Sample '*' can be used to set default contamination estimates." << endl
<< endl
<< "algorithmic features:" << endl
<< endl
<< " --report-genotype-likelihood-max" << endl
<< " Report genotypes using the maximum-likelihood estimate provided" << endl
<< " from genotype likelihoods." << endl
<< " -B --genotyping-max-iterations N" << endl
<< " Iterate no more than N times during genotyping step. default: 1000." << endl
<< " --genotyping-max-banddepth N" << endl
<< " Integrate no deeper than the Nth best genotype by likelihood when" << endl
<< " genotyping. default: 6." << endl
<< " -W --posterior-integration-limits N,M" << endl
<< " Integrate all genotype combinations in our posterior space" << endl
<< " which include no more than N samples with their Mth best" << endl
<< " data likelihood. default: 1,3." << endl
<< " -N --exclude-unobserved-genotypes" << endl
<< " Skip sample genotypings for which the sample has no supporting reads." << endl
<< " -S --genotype-variant-threshold N" << endl
<< " Limit posterior integration to samples where the second-best" << endl
<< " genotype likelihood is no more than log(N) from the highest" << endl
<< " genotype likelihood for the sample. default: ~unbounded" << endl
<< " -j --use-mapping-quality" << endl
<< " Use mapping quality of alleles when calculating data likelihoods." << endl
<< " -H --harmonic-indel-quality" << endl
<< " Use a weighted sum of base qualities around an indel, scaled by the" << endl
<< " distance from the indel. By default use a minimum BQ in flanking sequence." << endl
<< " -D --read-dependence-factor N" << endl
<< " Incorporate non-independence of reads by scaling successive" << endl
<< " observations by this factor during data likelihood" << endl
<< " calculations. default: 0.9" << endl
<< " -= --genotype-qualities" << endl
<< " Calculate the marginal probability of genotypes and report as GQ in" << endl
<< " each sample field in the VCF output." << endl
<< endl
<< "debugging:" << endl
<< endl
<< " -d --debug Print debugging output." << endl
<< " -dd Print more verbose debugging output (requires \"make DEBUG\")" << endl
<< endl
<< endl
<< "author: Erik Garrison <erik.garrison@gmail.com>" << endl
<< "version: " << VERSION_GIT << endl;
}
Parameters::Parameters(int argc, char** argv) {
if (argc == 1) {
simpleUsage(argv);
exit(1);
}
// record command line parameters
commandline = argv[0];
for (int i = 1; i < argc; ++i) {
commandline += " ";
commandline += argv[i];
}
// set defaults
// i/o parameters:
useStdin = false; // -c --stdin
fasta = ""; // -f --fasta-reference
targets = ""; // -t --targets
samples = ""; // -s --samples
populationsFile = "";
cnvFile = "";
output = "vcf"; // -v --vcf
outputFile = "";
gVCFout = false;
gVCFchunk = 0;
gVCFNoChunk = false; // --gvcf-no-chunk sets this to true
alleleObservationBiasFile = "";
// operation parameters
useDuplicateReads = false; // -E --use-duplicate-reads
suppressOutput = false; // -N --suppress-output
useBestNAlleles = 0; // -n --use-best-n-alleles
forceRefAllele = false; // -Z --use-reference-allele
useRefAllele = false; // .....
diploidReference = false; // -H --diploid-reference
allowIndels = true; // -i --no-indels
leftAlignIndels = true; // -O --dont-left-align-indels
allowMNPs = true; // -X --no-mnps
allowSNPs = true; // -I --no-snps
allowComplex = true;
strictVCF = false;
maxComplexGap = 3;
//maxHaplotypeLength = 100;
minRepeatSize = 5;
minRepeatEntropy = 1;
usePartialObservations = true;
pooledDiscrete = false; // -J --pooled
pooledContinuous = false;
ewensPriors = true;
permute = true; // -K --permute
useMappingQuality = false;
useMinIndelQuality = true;
obsBinomialPriors = true;
hwePriors = true;
alleleBalancePriors = true;
excludeUnobservedGenotypes = false;
excludePartiallyObservedGenotypes = false;
genotypeVariantThreshold = 0;
siteSelectionMaxIterations = 5;
reportGenotypeLikelihoodMax = false;
genotypingMaxIterations = 1000;
genotypingMaxBandDepth = 7;
minPairedAltCount = 0;
minAltMeanMapQ = 0;
limitGL = 0;
reportAllHaplotypeAlleles = false;
reportMonomorphic = false;
boundIndels = true; // ignore indels at ends of reads
standardGLs = false; // use experimental gls by default // XXX
MQR = 100; // -M --reference-mapping-quality
BQR = 60; // -B --reference-base-quality
ploidy = 2; // -p --ploidy
MQL0 = 1; // -m --min-mapping-quality
BQL0 = 0; // -q --min-base-quality
minSupportingAlleleQualitySum = 0;
minSupportingMappingQualitySum = 0;
BQL2 = 10; // -Q --mismatch-base-quality-threshold
RMU = 10000000; // -U --read-mismatch-limit
readMaxMismatchFraction = 1.0; // -z --read-max-mismatch-fraction
readSnpLimit = 10000000; // -$ --read-snp-limit
readIndelLimit = 10000000; // -e --read-indel-limit
IDW = -1; // -x --indel-exclusion-window
TH = 10e-3; // -T --theta
PVL = 0.0; // -P --pvar
RDF = 0.9; // -D --read-dependence-factor
diffusionPriorScalar = 1.0; // -V --diffusion-prior-scalar
WB = 1; // -W --posterior-integration-limits
TB = 3;
posteriorIntegrationDepth = 0;
calculateMarginals = false;
minAltFraction = 0.05; // require 5% of reads from sample to be supporting the same alternate to consider
minAltCount = 2; // require 2 reads in same sample call
minAltTotal = 1;
minAltQSum = 0;
baseQualityCap = 0;
probContamination = 10e-9;
//minAltQSumTotal = 0;
minCoverage = 0;
limitCoverage = 0;
skipCoverage = 0;
trimComplexTail = 0;
debuglevel = 0;
debug = false;
debug2 = false;
showReferenceRepeats = false;
int c; // counter for getopt
static const struct option long_options[] =
{
{"help", no_argument, 0, 'h'},
{"version", no_argument, 0, '#'},
{"bam", required_argument, 0, 'b'},
{"bam-list", required_argument, 0, 'L'},
{"stdin", no_argument, 0, 'c'},
{"fasta-reference", required_argument, 0, 'f'},
{"targets", required_argument, 0, 't'},
{"region", required_argument, 0, 'r'},
{"samples", required_argument, 0, 's'},
{"populations", required_argument, 0, '2'},
{"cnv-map", required_argument, 0, 'A'},
{"vcf", required_argument, 0, 'v'},
{"gvcf", no_argument, 0, '8'},
{"gvcf-chunk", required_argument, 0, '&'},
{"gvcf-dont-use-chunk", required_argument, 0 , '&'},
{"use-duplicate-reads", no_argument, 0, '4'},
{"no-partial-observations", no_argument, 0, '['},
{"use-best-n-alleles", required_argument, 0, 'n'},
{"use-reference-allele", no_argument, 0, 'Z'},
{"harmonic-indel-quality", no_argument, 0, 'H'},
{"standard-filters", no_argument, 0, '0'},
{"reference-quality", required_argument, 0, '1'},
{"ploidy", required_argument, 0, 'p'},
{"pooled-discrete", no_argument, 0, 'J'},
{"pooled-continuous", no_argument, 0, 'K'},
{"no-population-priors", no_argument, 0, 'k'},
{"use-mapping-quality", no_argument, 0, 'j'},
{"min-mapping-quality", required_argument, 0, 'm'},
{"min-base-quality", required_argument, 0, 'q'},
{"min-supporting-allele-qsum", required_argument, 0, 'R'},
{"min-supporting-mapping-qsum", required_argument, 0, 'Y'},
{"mismatch-base-quality-threshold", required_argument, 0, 'Q'},
{"read-mismatch-limit", required_argument, 0, 'U'},
{"read-max-mismatch-fraction", required_argument, 0, 'z'},
{"read-snp-limit", required_argument, 0, '$'},
{"read-indel-limit", required_argument, 0, 'e'},
{"throw-away-indel-obs", no_argument, 0, 'i'},
{"dont-left-align-indels", no_argument, 0, 'O'},
{"throw-away-mnps-obs", no_argument, 0, 'X'},
{"throw-away-complex-obs", no_argument, 0, 'u'},
{"max-complex-gap", required_argument, 0, 'E'},
{"haplotype-length", required_argument, 0, 'E'},
{"min-repeat-size", required_argument, 0, 'E'},
{"min-repeat-entropy", required_argument, 0, 'E'},
{"throw-away-snp-obs", no_argument, 0, 'I'},
{"indel-exclusion-window", required_argument, 0, 'x'},
{"theta", required_argument, 0, 'T'},
{"pvar", required_argument, 0, 'P'},
{"strict-vcf", no_argument, 0, '/'},
{"read-dependence-factor", required_argument, 0, 'D'},
{"binomial-obs-priors-off", no_argument, 0, 'V'},
{"allele-balance-priors-off", no_argument, 0, 'a'},
{"hwe-priors-off", no_argument, 0, 'w'},
{"posterior-integration-limits", required_argument, 0, 'W'},
{"min-alternate-fraction", required_argument, 0, 'F'},
{"min-alternate-count", required_argument, 0, 'C'},
//{"min-paired-alternate-count", required_argument, 0, 'Y'},
{"observation-bias", required_argument, 0, '%'},
{"min-alternate-total", required_argument, 0, 'G'},
//{"min-alternate-mean-mapq", required_argument, 0, 'k'},
{"min-alternate-qsum", required_argument, 0, '3'},
{"min-coverage", required_argument, 0, '!'},
{"limit-coverage", required_argument, 0, '+'},
{"skip-coverage", required_argument, 0, 'g'},
{"trim-complex-tail", no_argument, 0, ']'},
{"genotype-qualities", no_argument, 0, '='},
{"variant-input", required_argument, 0, '@'},
{"only-use-input-alleles", no_argument, 0, 'l'},
//{"show-reference-repeats", no_argument, 0, '_'},
{"exclude-unobserved-genotypes", no_argument, 0, 'N'},
{"genotype-variant-threshold", required_argument, 0, 'S'},
{"site-selection-max-iterations", required_argument, 0, 'M'},
{"genotyping-max-iterations", required_argument, 0, 'B'},
{"genotyping-max-banddepth", required_argument, 0, '7'},
{"haplotype-basis-alleles", required_argument, 0, '9'},
{"report-genotype-likelihood-max", no_argument, 0, '5'},
{"report-all-haplotype-alleles", no_argument, 0, '6'},
{"base-quality-cap", required_argument, 0, '('},
{"legacy-gls", no_argument, 0, ')'},
{"prob-contamination", required_argument, 0, '_'},
{"contamination-estimates", required_argument, 0, ','},
{"report-monomorphic", no_argument, 0, '6'},
{"debug", no_argument, 0, 'd'},
{0, 0, 0, 0}
};
while (true) {
int option_index = 0;
c = getopt_long(argc, argv, "hcO4ZKjH[0diN5a)Ik=wl6#uVXJY:b:G:M:x:@:A:f:t:r:s:v:n:B:p:m:q:R:Q:U:$:e:T:P:D:^:S:W:F:C:&:L:8z:1:3:E:7:2:9:%:_:,:(:!:+:g:",
long_options, &option_index);
if (c == -1) // end of options
break;
switch (c) {
// i/o parameters:
// -b --bam
case 'b':
bams.push_back(optarg);
break;
// -c --stdin
case 'c':
useStdin = true;
bams.push_back("stdin");
break;
// -f --fasta-reference
case 'f':
fasta = optarg;
break;
// -t --targets
case 't':
targets = optarg;
break;
// -r --region
case 'r':
regions.push_back(optarg);
break;
// -s --samples
case 's':
samples = optarg;
break;
// --populations
case '2':
populationsFile = optarg;
break;
// -A --cnv-file
case 'A':
cnvFile = optarg;
break;
// -j --use-mapping-quality
case 'j':
useMappingQuality = true;
break;
// -v --vcf
case 'v':
output = "vcf";
outputFile = optarg;
break;
// -O --dont-left-align-indels
case 'O':
leftAlignIndels = false;
break;
// --bam-list
case 'L':
addLinesFromFile(bams, string(optarg));
break;
// -8 --gvcf
case '8':
gVCFout = true;
break;
// -& BOOL/INT --gvcf-no-chunk BOOL/INT --gvcf-chunk
case '&':
//cerr << "optarg:\t" << optarg << endl;
if(optarg[0] == 't'){
gVCFNoChunk = true;
} else if (optarg[0] == 'f'){
gVCFNoChunk = false;
} else {
gVCFchunk = atoi(optarg);
}
break;
// -4 --use-duplicate-reads
case '4':
useDuplicateReads = true;
break;
// -3 --min-alternate-qsum
case '3':
if (!convert(optarg, minAltQSum)) {
cerr << "could not parse min-alternate-qsum" << endl;
exit(1);
}
break;
// -G --min-alternate-total
case 'G':
if (!convert(optarg, minAltTotal)) {
cerr << "could not parse min-alternate-total" << endl;
exit(1);
}
break;
// -! --min-coverage
case '!':
if (!convert(optarg, minCoverage)) {
cerr << "could not parse min-coverage" << endl;
exit(1);
}
break;
// -+ --limit-coverage
case '+':
if (!convert(optarg, limitCoverage)) {
cerr << "could not parse limit-coverage" << endl;
exit(1);
}
break;
// -g --skip-coverage
case 'g':
if (!convert(optarg, skipCoverage)) {
cerr << "could not parse skip-coverage" << endl;
exit(1);
}
break;
// --trim-complex-tail
case ']':
trimComplexTail = true;
break;
// -n --use-best-n-alleles
case 'n':
if (!convert(optarg, useBestNAlleles)) {
cerr << "could not parse use-best-n-alleles" << endl;
exit(1);
}
break;
// -Z --use-reference-allele
case 'Z':
forceRefAllele = true;
useRefAllele = true;
break;
// -H --harmonic-indel-quality
case 'H':
useMinIndelQuality = false;
break;
// -0 --standard-filters
case '0':
MQL0 = 30;
BQL0 = 20;
break;
// -M --expectation-maximization
case 'M':
if (!convert(optarg, siteSelectionMaxIterations)) {
cerr << "could not parse site-selection-max-iterations" << endl;
exit(1);
}
break;
case '/':
strictVCF = true;
break;
case 'u':
allowComplex = false;
break;
case 'E':
{
string arg(argv[optind - 2]);
if (arg == "--min-repeat-size") {
if (!convert(optarg, minRepeatSize)) {
cerr << "could not parse " << arg << endl;
exit(1);
}
} else if (arg == "--min-repeat-entropy") {
if (!convert(optarg, minRepeatEntropy)) {
cerr << "could not parse " << arg << endl;
exit(1);
}
} else {
if (!convert(optarg, maxComplexGap)) {
cerr << "could not parse maxComplexGap" << endl;
exit(1);
}
}
break;
}
// -B --genotyping-max-iterations
case 'B':
if (!convert(optarg, genotypingMaxIterations)) {
cerr << "could not parse genotyping-max-iterations" << endl;
exit(1);
}
break;
// -7 --genotyping-max-banddepth
case '7':
if (!convert(optarg, genotypingMaxBandDepth)) {
cerr << "could not parse genotyping-max-iterations" << endl;
exit(1);
}
break;
// -1 --reference-quality
case '1':
if (!convert(split(optarg, ",").front(), MQR)) {
cerr << "could not parse reference mapping quality" << endl;
exit(1);
}
if (!convert(split(optarg, ",").back(), BQR)) {
cerr << "could not parse reference base quality" << endl;
exit(1);
}
break;
// -p --ploidy
case 'p':
if (!convert(optarg, ploidy)) {
cerr << "could not parse ploidy" << endl;
exit(1);
}
if (ploidy <= 0) {
cerr << "cannot set ploidy to less than 1" << endl;
exit(1);
}
break;
case 'J':
pooledDiscrete = true;
hwePriors = false; // disable hwe sampling prob when using discrete pooling
break;
// -m --min-mapping-quality
case 'm':
if (!convert(optarg, MQL0)) {
cerr << "could not parse min-mapping-quality" << endl;
exit(1);
}
break;
// -q --min-base-quality
case 'q':
if (!convert(optarg, BQL0)) {
cerr << "could not parse min-base-quality" << endl;
exit(1);
}
break;
// -R --min-supporting-allele-qsum
case 'R':
if (!convert(optarg, minSupportingAlleleQualitySum)) {
cerr << "could not parse min-supporting-allele-qsum" << endl;
exit(1);
}
break;
// -Y --min-supporting-mapping-quality
case 'Y':
if (!convert(optarg, minSupportingMappingQualitySum)) {
cerr << "could not parse min-supporting-mapping-qsum" << endl;
exit(1);
}
break;
// -N --exclude-unobserved-genotypes
case 'N':
excludeUnobservedGenotypes = true;
break;
// -S --genotype-variant-threshold
case 'S':
if (!convert(optarg, genotypeVariantThreshold)) {
cerr << "could not parse genotype-variant-threshold" << endl;
exit(1);
}
break;
case '5':
reportGenotypeLikelihoodMax = true;
break;
// -Q --mismatch-base-quality-threshold
case 'Q':
if (!convert(optarg, BQL2)) {
cerr << "could not parse mismatch-base-quality-threshold" << endl;
exit(1);
}
break;
// -U --read-mismatch-limit
case 'U':
if (!convert(optarg, RMU)) {
cerr << "could not parse read-mismatch-limit" << endl;
exit(1);
}
break;
// -z --read-max-mismatch-fraction
case 'z':
if (!convert(optarg, readMaxMismatchFraction)) {
cerr << "could not parse read-mismatch-limit" << endl;
exit(1);
}
break;
// -$ --read-snp-limit
case '$':
if (!convert(optarg, readSnpLimit)) {
cerr << "could not parse read-snp-limit" << endl;
exit(1);
}
break;
// -e --read-indel-limit
case 'e':
if (!convert(optarg, readIndelLimit)) {
cerr << "could not parse read-indel-limit" << endl;
exit(1);
}
break;
// -x --indel-exclusion-window
case 'x':
if (!convert(optarg, IDW)) {
cerr << "could not parse indel-exclusion-window" << endl;
exit(1);
}
break;
// -i --indels
case 'i':
allowIndels = false;
break;
// -X --mnps
case 'X':
allowMNPs = false;
break;
// -I --no-snps
case 'I':
allowSNPs = false;
break;
// -T --theta
case 'T':
if (!convert(optarg, TH)) {
cerr << "could not parse theta" << endl;
exit(1);
}
break;
// -P --pvar
case 'P':
if (!convert(optarg, PVL)) {
cerr << "could not parse pvar" << endl;
exit(1);
}
break;
// -D --read-dependence-factor
case 'D':
if (!convert(optarg, RDF)) {
cerr << "could not parse read-dependence-factor" << endl;
exit(1);
}
break;
// -% --observation-bias
case '%':
alleleObservationBiasFile = optarg;
break;
// observation priors
case 'V':
obsBinomialPriors = false;
break;
// allele balance
case 'a':
alleleBalancePriors = false;
break;
// hwe expectations
case 'w':
hwePriors = false;
break;
// -W --posterior-integration-limits
case 'W':
if (!convert(split(optarg, ",").front(), WB)) {
cerr << "could not parse posterior-integration-limits (bandwidth)" << endl;
exit(1);
}
if (!convert(split(optarg, ",").back(), TB)) {
cerr << "could not parse posterior-integration-limits (banddepth)" << endl;
exit(1);
}
break;
// -F --min-alternate-fraction
case 'F':
if (!convert(optarg, minAltFraction)) {
cerr << "could not parse min-alternate-fraction" << endl;
exit(1);
}
break;
// -C --min-alternate-count
case 'C':
if (!convert(optarg, minAltCount)) {
cerr << "could not parse min-alternate-count" << endl;
exit(1);
}
break;
// -k --no-population-priors
case 'k':
pooledDiscrete = true;
ewensPriors = false;
hwePriors = false;
break;
case 'K':
pooledContinuous = true;
break;
case '=':
calculateMarginals = true;
break;
case '@':
variantPriorsFile = optarg;
break;
case '9':
haplotypeVariantFile = optarg;
break;
case 'l':
break;
case '6':
{
string arg(argv[optind - 1]);
if (arg == "--report-monomorphic") {
reportMonomorphic = true;
}
reportAllHaplotypeAlleles = true;
}
break;
case '[':
usePartialObservations = false;
break;
case '_':
if (!convert(optarg, probContamination)) {
cerr << "could not parse prob-contamination" << endl;
exit(1);
}
break;
case ',':
contaminationEstimateFile = optarg;
break;
case ')':
standardGLs = true;
break;
case '(':
if (!convert(optarg, baseQualityCap)) {
cerr << "could not parse base-quality-cap" << endl;
exit(1);
}
break;
// -d --debug
case 'd':
++debuglevel;
break;
case '#':
// --version
cout << "version: " << VERSION_GIT << endl;
exit(0);
break;
case 'h':
usage(argv);
exit(0);
break;
// either catch "long options" or
case '?': // print a suggestion about the most-likely long option which the argument matches
{
string bad_arg(argv[optind - 1]);
const option* opt = &long_options[0];
const option* closest_opt = opt;
int shortest_distance = levenshteinDistance(opt->name, bad_arg);
++opt;
while (opt->name != 0) {
int distance = levenshteinDistance(opt->name, bad_arg);
if (distance < shortest_distance) {
shortest_distance = distance;
closest_opt = opt;
}
++opt;
}
cerr << "did you mean --" << closest_opt->name << " ?" << endl;
exit(1);
}
break;
default:
abort ();
}
}
// any remaining arguments are considered as bam files
if (optind < argc) {
if (useStdin) {
cerr << "--stdin flag specified, but a list of BAM files given. Jumping disabled." << endl;
}
while (optind < argc) {
bams.push_back(argv[optind++]);
}
}
if (debuglevel >= 1) {
debug = true;
}
if (debuglevel >= 2) {
debug2 = true;
}
if (bams.size() == 0) {
cerr << "Please specify a BAM file or files." << endl;
exit(1);
}
if (fasta == "") {
cerr << "Please specify a fasta reference file." << endl;
exit(1);
}
// check that there aren't duplicates in the bams list
for( int i=1; i<bams.size(); ++i ){
for( int j=0; j<i; ++j ){
if( bams[i] == bams[j] ){
cerr << "Error: Duplicate bam file '" << bams[i] << "'" << endl;
exit(1);
}
}
}
}
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