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Bug fixes for integration test, use correct new UG syntax

This commit is contained in:
Guillermo del Angel 2012-07-17 16:57:59 -04:00
parent 40b8c7172c
commit 731bbba2e6
3 changed files with 6 additions and 6 deletions
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4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/PoolCallerIntegrationTest.java
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@ -24,14 +24,14 @@ public class PoolCallerIntegrationTest extends WalkerTest {
final String NA12878_WG_CALLS = comparisonDataLocation + "Unvalidated/NA12878/CEUTrio.HiSeq.WGS.b37_decoy.recal.ts_95.snp_indel_combined.vcf";
final String LSV_ALLELES = validationDataLocation + "ALL.chr20_40m_41m.largeScaleValidationSites.vcf";
private void PC_MT_Test(String bam, String args, String name, String md5) {
final String base = String.format("-T UnifiedGenotyper -R %s -I %s -L %s -reference_sample_calls %s -refsample %s -glm POOLSNP -ignoreLane -pnrm POOL",
final String base = String.format("-T UnifiedGenotyper -R %s -I %s -L %s --reference_sample_calls %s -refsample %s -glm POOLSNP -ignoreLane -pnrm POOL",
REF, bam, MTINTERVALS, REFSAMPLE_MT_CALLS, REFSAMPLE_NAME) + " --no_cmdline_in_header -o %s";
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
executeTest("testPoolCaller:"+name+" args=" + args, spec);
}
private void PC_LSV_Test(String args, String name, String model, String md5) {
final String base = String.format("-T UnifiedGenotyper -R %s -I %s -L %s -reference_sample_calls %s -refsample %s -glm %s -ignoreLane -pnrm POOL",
final String base = String.format("-T UnifiedGenotyper -R %s -I %s -L %s --reference_sample_calls %s -refsample %s -glm %s -ignoreLane -pnrm POOL",
REF, LSV_BAM, LSVINTERVALS, NA12878_WG_CALLS, REFSAMPLE_NAME, model) + " --no_cmdline_in_header -o %s";
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
executeTest("testPoolCaller:"+name+" args=" + args, spec);

6
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
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@ -277,7 +277,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tMLE\tMAP");
annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, VariantContextUtils.DEFAULT_PLOIDY);
UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, UAC.samplePloidy);
// initialize the header
Set<VCFHeaderLine> headerInfo = getHeaderInfo(UAC, annotationEngine, dbsnp);
@ -309,8 +309,8 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
// add the pool values for each genotype
if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) {
headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the alt allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed, for this sample (equivalent to sample genotype in diploid case)"));
headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed, for this sample (equivalent to sample genotype in diploid case)"));
headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed, for this pool"));
headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed, for this pool"));
}
if (UAC.referenceSampleName != null) {
headerInfo.add(new VCFInfoHeaderLine(VCFConstants.REFSAMPLE_DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Total reference sample depth"));

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -115,7 +115,7 @@ public class UnifiedGenotyperEngine {
// ---------------------------------------------------------------------------------------------------------
@Requires({"toolkit != null", "UAC != null"})
public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), VariantContextUtils.DEFAULT_PLOIDY*(SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()).size()));
this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), VariantContextUtils.DEFAULT_PLOIDY);
}
@Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0","ploidy>0"})