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Removing argument from HaplotypeCaller that was made unneccesary by recent improvements to triggering around large events

This commit is contained in:
Ryan Poplin 2012-08-08 15:13:20 -04:00
parent 0a2a646a52
commit 1223d77546
2 changed files with 14 additions and 25 deletions
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35
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
View File

@ -128,9 +128,11 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@Argument(fullName="minPruning", shortName="minPruning", doc = "The minimum allowed pruning factor in assembly graph. Paths with <= X supporting kmers are pruned from the graph", required = false)
protected int MIN_PRUNE_FACTOR = 1;
@Advanced
@Argument(fullName="genotypeFullActiveRegion", shortName="genotypeFullActiveRegion", doc = "If specified, alternate alleles are considered to be the full active region for the purposes of genotyping", required = false)
protected boolean GENOTYPE_FULL_ACTIVE_REGION = false;
@Advanced
@Argument(fullName="fullHaplotype", shortName="fullHaplotype", doc = "If specified, output the full haplotype sequence instead of converting to individual variants w.r.t. the reference", required = false)
protected boolean OUTPUT_FULL_HAPLOTYPE_SEQUENCE = false;
@ -141,9 +143,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@Argument(fullName="downsampleRegion", shortName="dr", doc="coverage, per-sample, to downsample each active region to", required = false)
protected int DOWNSAMPLE_PER_SAMPLE_PER_REGION = 1000;
@Argument(fullName="useExpandedTriggerSet", shortName="expandedTriggers", doc = "If specified, use additional, experimental triggers designed to capture larger indels but which may lead to an increase in the false positive rate", required=false)
protected boolean USE_EXPANDED_TRIGGER_SET = false;
@Argument(fullName="useAllelesTrigger", shortName="allelesTrigger", doc = "If specified, use additional trigger on variants found in an external alleles file", required=false)
protected boolean USE_ALLELES_TRIGGER = false;
@ -245,8 +244,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC.clone(), logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_VARIANTS_ONLY; // low values used for isActive determination only, default/user-specified values used for actual calling
UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.DISCOVERY; // low values used for isActive determination only, default/user-specified values used for actual calling
UAC.STANDARD_CONFIDENCE_FOR_CALLING = (USE_EXPANDED_TRIGGER_SET ? 0.3 : Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_CALLING) ); // low values used for isActive determination only, default/user-specified values used for actual calling
UAC.STANDARD_CONFIDENCE_FOR_EMITTING = (USE_EXPANDED_TRIGGER_SET ? 0.3 : Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING) ); // low values used for isActive determination only, default/user-specified values used for actual calling
UAC.STANDARD_CONFIDENCE_FOR_CALLING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_CALLING);
UAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.max( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING);
UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
// initialize the output VCF header
@ -332,29 +331,19 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
final Map<String, AlignmentContext> splitContexts = AlignmentContextUtils.splitContextBySampleName(context);
final GenotypesContext genotypes = GenotypesContext.create(splitContexts.keySet().size());
final MathUtils.RunningAverage averageHQSoftClips = new MathUtils.RunningAverage();
for( Map.Entry<String, AlignmentContext> sample : splitContexts.entrySet() ) {
for( final Map.Entry<String, AlignmentContext> sample : splitContexts.entrySet() ) {
final double[] genotypeLikelihoods = new double[3]; // ref versus non-ref (any event)
Arrays.fill(genotypeLikelihoods, 0.0);
for( final PileupElement p : sample.getValue().getBasePileup() ) {
final byte qual = ( USE_EXPANDED_TRIGGER_SET ?
( p.isNextToSoftClip() || p.isBeforeInsertion() || p.isAfterInsertion() ? ( p.getQual() > QualityUtils.MIN_USABLE_Q_SCORE ? p.getQual() : (byte) 20 ) : p.getQual() )
: p.getQual() );
if( p.isDeletion() || qual > (USE_EXPANDED_TRIGGER_SET ? QualityUtils.MIN_USABLE_Q_SCORE : (byte) 18) ) {
final byte qual = p.getQual();
if( p.isDeletion() || qual > (byte) 18) {
int AA = 0; final int AB = 1; int BB = 2;
if( USE_EXPANDED_TRIGGER_SET ) {
if( p.getBase() != ref.getBase() || p.isDeletion() || p.isBeforeDeletedBase() || p.isAfterDeletedBase() || p.isBeforeInsertion() || p.isAfterInsertion() || p.isNextToSoftClip() ||
(!p.getRead().getNGSPlatform().equals(NGSPlatform.SOLID) && ((p.getRead().getReadPairedFlag() && p.getRead().getMateUnmappedFlag()) || BadMateFilter.hasBadMate(p.getRead()))) ) {
AA = 2;
BB = 0;
}
} else {
if( p.getBase() != ref.getBase() || p.isDeletion() || p.isBeforeDeletedBase() || p.isAfterDeletedBase() || p.isBeforeInsertion() || p.isAfterInsertion() || p.isNextToSoftClip() ) {
AA = 2;
BB = 0;
if( p.isNextToSoftClip() ) {
averageHQSoftClips.add(AlignmentUtils.calcNumHighQualitySoftClips(p.getRead(), (byte) 28));
}
if( p.getBase() != ref.getBase() || p.isDeletion() || p.isBeforeDeletedBase() || p.isAfterDeletedBase() || p.isBeforeInsertion() || p.isAfterInsertion() || p.isNextToSoftClip() ) {
AA = 2;
BB = 0;
if( p.isNextToSoftClip() ) {
averageHQSoftClips.add(AlignmentUtils.calcNumHighQualitySoftClips(p.getRead(), (byte) 28));
}
}
genotypeLikelihoods[AA] += p.getRepresentativeCount() * QualityUtils.qualToProbLog10(qual);

4
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
View File

@ -246,9 +246,9 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
}
/**
* Initialize the reduce step by creating a PrintStream from the filename specified as an argument to the walker.
* Initialize the reduce step by returning 0L
*
* @return returns A PrintStream created from the -recalFile filename argument specified to the walker
* @return returns 0L
*/
public Long reduceInit() {
return 0L;