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Small improvements to the pileup arguments #8050

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Dec 23, 2022
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Small improvements to the pileup arguments #8050

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21 changes: 11 additions & 10 deletions ...institute/hellbender/tools/walkers/haplotypecaller/PileupDetectionArgumentCollection.java
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Expand Up @@ -49,49 +49,50 @@ public final class PileupDetectionArgumentCollection {

@Advanced
@Hidden
@Argument(fullName= "num-artificial-haplotypes-to-add-per-allele", doc = "Pileup Detection: This argument limits the maximum number of novel haplotypes to be added to the assembly haplotypes per pileup allele added. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"'` argument)", optional = true)
@Argument(fullName= "num-artificial-haplotypes-to-add-per-allele",
doc = "Pileup Detection: This argument limits the maximum number of novel haplotypes to be added to the assembly haplotypes per pileup allele added. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"'` argument)", optional = true, minValue = 0)
public int numHaplotypesToIterate = 5;
@Advanced
@Hidden
@Argument(fullName= "artifical-haplotype-filtering-kmer-size", doc = "Pileup Detection: Controls what size to kmerize reads to in order to select best supported artificial haplotypes. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)
@Argument(fullName= "artifical-haplotype-filtering-kmer-size", doc = "Pileup Detection: Controls what size to kmerize reads to in order to select best supported artificial haplotypes. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true, minValue = 0)
public int filteringKmerSize = 10;

/**
* Percentage of reads required to support the alt for a variant to be considered
*/
@Hidden
@Argument(fullName= PILEUP_DETECTION_SNP_THRESHOLD, doc = "Pileup Detection: Percentage of alt supporting reads in order to consider alt SNP. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)
@Argument(fullName= PILEUP_DETECTION_SNP_THRESHOLD, doc = "Pileup Detection: Fraction of alt supporting reads in order to consider alt SNP. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true, minValue = 0D, maxValue = 1D)
public double snpThreshold = 0.1;
@Hidden
@Argument(fullName= PILEUP_DETECTION_INDEL_THRESHOLD, doc = "Pileup Detection: Percentage of alt supporting reads in order to consider alt indel. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)
@Argument(fullName= PILEUP_DETECTION_INDEL_THRESHOLD, doc = "Pileup Detection: Fraction of alt supporting reads in order to consider alt indel. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true, minValue = 0D, maxValue = 1D)
public double indelThreshold = 0.5;

@Hidden
@Argument(fullName= PILEUP_DETECTION_ABSOLUTE_ALT_DEPTH, doc = "Pileup Detection: Absolute number of alt reads necessary to be included in pileup events. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)
@Argument(fullName= PILEUP_DETECTION_ABSOLUTE_ALT_DEPTH, doc = "Pileup Detection: Absolute number of alt reads necessary to be included in pileup events. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true, minValue = 0D)
public double pileupAbsoluteDepth = 0;
@Hidden
@Argument(fullName= PILEUP_DETECTION_INDEL_SNP_BLOCKING_RANGE, doc = "Pileup Detection: Filters out pileup snps within this many bases of an assembled indel. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)
@Argument(fullName= PILEUP_DETECTION_INDEL_SNP_BLOCKING_RANGE, doc = "Pileup Detection: Filters out pileup snps within this many bases of an assembled indel. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true, minValue = 0D)
public int snpAdajacentToAssemblyIndel = 5;

/**
* Arguments related to the "bad read filtering" where alleles that are supported primarily by reads that fail at least one of a number of heuristics will be filtered out
*/
@Hidden
@Argument(fullName= PILEUP_DETECTION_BAD_READ_RATIO_LONG_NAME, doc = "Pileup Detection: Threshold of Alt reads rejected by bad reads heuristics to allow the variant. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)
@Argument(fullName= PILEUP_DETECTION_BAD_READ_RATIO_LONG_NAME, doc = "Pileup Detection: Threshold of ratio of Alt reads rejected by bad reads heuristics to allow the variant. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true, minValue = 0D, maxValue = 1D)
public double badReadThreshold = 0.0;
@Hidden
@Argument(fullName= PILEUP_DETECTION_PROPER_PAIR_READ_BADNESS_LONG_NAME, doc = "Pileup Detection: Reject alt reads not in proper-pairs. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)
public boolean badReadProperPair = true;
@Hidden
@Argument(fullName= PILEUP_DETECTION_EDIT_DISTANCE_BADNESS_LONG_NAME, doc = "Pileup Detection: Reject alt reads with greater than this fraction of mismatching bases from the reference (proxied using the NM tag). (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)
@Argument(fullName= PILEUP_DETECTION_EDIT_DISTANCE_BADNESS_LONG_NAME, doc = "Pileup Detection: Reject alt reads with greater than this fraction of mismatching bases from the reference (proxied using the NM tag). (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true, minValue = 0D, maxValue = 1D)
public double badReadEditDistance = 0.08;
@Hidden
@Argument(fullName= PILEUP_DETECTION_CHIMERIC_READ_BADNESS_LONG_NAME, doc = "Pileup Detection: Reject reads that are chimeric or supplementary. (Requires '--"+PILEUP_DETECTION_LONG_NAME+"' argument)", optional = true)
public boolean badReadSecondaryOrSupplementary = true;
@Hidden
@Argument(fullName= PILEUP_DETECTION_TLEN_MEAN_LONG_NAME, doc = "Pileup Detection: Mean template length (T LEN) to consider for read badness. Requires '--"+PILEUP_DETECTION_TLEN_STD_LONG_NAME+"' to also be set.", optional = true)
@Argument(fullName= PILEUP_DETECTION_TLEN_MEAN_LONG_NAME, doc = "Pileup Detection: Mean template length (T LEN) to consider for read badness. Requires '--"+PILEUP_DETECTION_TLEN_STD_LONG_NAME+"' to also be set.", optional = true, minValue = 0D)
public double templateLengthMean = 0.0;
@Hidden
@Argument(fullName= PILEUP_DETECTION_TLEN_STD_LONG_NAME, doc = "Pileup Detection: Standard deviation template length (T LEN) to consider for read badness. Requires '--"+PILEUP_DETECTION_TLEN_MEAN_LONG_NAME+"' to also be set.", optional = true)
@Argument(fullName= PILEUP_DETECTION_TLEN_STD_LONG_NAME, doc = "Pileup Detection: Standard deviation template length (T LEN) to consider for read badness. Requires '--"+PILEUP_DETECTION_TLEN_MEAN_LONG_NAME+"' to also be set.", optional = true, minValue = 0D)
public double templateLengthStd = 0.0;
}