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Pool caller improvements: a) Log ref sample depth at every called site (will add more ref-related annotations later), b) Make -glm POOLBOTH work in case we want to genotype snp's and indels together, c) indel bug fix (pool and non-pool): prevent a bad GenomeLoc to be formed if we're running GGA and incoming alleles are larger than ref window size (typically 400 bb)

This commit is contained in:
Guillermo del Angel 2012-06-29 11:06:12 -04:00
parent 9346c5b37a
commit 5a9a37ba01
2 changed files with 16 additions and 8 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -186,7 +186,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
final int hsize = ref.getWindow().size() - Math.abs(eventLength) - 1; final int hsize = ref.getWindow().size() - Math.abs(eventLength) - 1;
final int numPrefBases = ref.getLocus().getStart() - ref.getWindow().getStart() + 1; final int numPrefBases = ref.getLocus().getStart() - ref.getWindow().getStart() + 1;
haplotypeMap.putAll(Haplotype.makeHaplotypeListFromAlleles(alleleList, loc.getStart(), if (hsize <= 0) // protect against event lengths larger than ref window sizes
haplotypeMap.clear();
else
haplotypeMap.putAll(Haplotype.makeHaplotypeListFromAlleles(alleleList, loc.getStart(),
ref, hsize, numPrefBases)); ref, hsize, numPrefBases));
} }
} }

19
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -367,6 +367,8 @@ public class UnifiedGenotyperEngine {
// *** note that calculating strand bias involves overwriting data structures, so we do that last // *** note that calculating strand bias involves overwriting data structures, so we do that last
final HashMap<String, Object> attributes = new HashMap<String, Object>(); final HashMap<String, Object> attributes = new HashMap<String, Object>();
// inherit attributed from input vc
attributes.putAll(vc.getAttributes());
// if the site was downsampled, record that fact // if the site was downsampled, record that fact
if ( !limitedContext && rawContext.hasPileupBeenDownsampled() ) if ( !limitedContext && rawContext.hasPileupBeenDownsampled() )
attributes.put(VCFConstants.DOWNSAMPLED_KEY, true); attributes.put(VCFConstants.DOWNSAMPLED_KEY, true);
@ -581,6 +583,9 @@ public class UnifiedGenotyperEngine {
final AlignmentContext rawContext) { final AlignmentContext rawContext) {
final List<GenotypeLikelihoodsCalculationModel.Model> models = new ArrayList<GenotypeLikelihoodsCalculationModel.Model>(2); final List<GenotypeLikelihoodsCalculationModel.Model> models = new ArrayList<GenotypeLikelihoodsCalculationModel.Model>(2);
String modelPrefix = "";
if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") )
modelPrefix = UAC.GLmodel.name().toUpperCase().replaceAll("BOTH","");
// if we're genotyping given alleles and we have a requested SNP at this position, do SNP // if we're genotyping given alleles and we have a requested SNP at this position, do SNP
if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) { if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
@ -590,24 +595,24 @@ public class UnifiedGenotyperEngine {
if ( vcInput.isSNP() ) { if ( vcInput.isSNP() ) {
// ignore SNPs if the user chose INDEL mode only // ignore SNPs if the user chose INDEL mode only
if ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH ) if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") )
models.add(GenotypeLikelihoodsCalculationModel.Model.SNP); models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
else if ( UAC.GLmodel.name().toUpperCase().contains("SNP") ) else if ( UAC.GLmodel.name().toUpperCase().contains("SNP") )
models.add(UAC.GLmodel); models.add(UAC.GLmodel);
} }
else if ( vcInput.isIndel() || vcInput.isMixed() ) { else if ( vcInput.isIndel() || vcInput.isMixed() ) {
// ignore INDELs if the user chose SNP mode only // ignore INDELs if the user chose SNP mode only
if ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH ) if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") )
models.add(GenotypeLikelihoodsCalculationModel.Model.INDEL); models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"INDEL"));
else if (UAC.GLmodel.name().toUpperCase().contains("INDEL")) else if (UAC.GLmodel.name().toUpperCase().contains("INDEL"))
models.add(UAC.GLmodel); models.add(UAC.GLmodel);
} }
// No support for other types yet // No support for other types yet
} }
else { else {
if ( UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.BOTH ) { if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") ) {
models.add(GenotypeLikelihoodsCalculationModel.Model.SNP); models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
models.add(GenotypeLikelihoodsCalculationModel.Model.INDEL); models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"INDEL"));
} }
else { else {
models.add(UAC.GLmodel); models.add(UAC.GLmodel);