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Finished draft of code for new map-combine-reduce annotation framework 

All VQSR annotations can be generated in allele-specific mode
Pull out allele-specific annotations in AS_Standard annotation group
This commit is contained in:
Laura Gauthier 2015-06-11 10:52:23 -04:00
parent fcaf37279c
commit 68a2f1243d
3 changed files with 4 additions and 4 deletions
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2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
View File

@ -316,7 +316,7 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations() {
final String commandLine = String.format("-T HaplotypeCaller --pcr_indel_model NONE -pairHMMSub %s %s -R %s -I %s -L %s -ERC GVCF --no_cmdline_in_header -variant_index_type %s -variant_index_parameter %d -G Standard -G AS_Standard --disableDithering",
HMM_SUB_IMPLEMENTATION, ALWAYS_LOAD_VECTOR_HMM, b37KGReference, privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam", "20:10433000-10437000", GATKVCFUtils.DEFAULT_GVCF_INDEX_TYPE, GATKVCFUtils.DEFAULT_GVCF_INDEX_PARAMETER);
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("9a2887ed7afa829a75ec7d6e11dfc45f"));
final WalkerTestSpec spec = new WalkerTestSpec(commandLine + " -o %s", Arrays.asList("fc10e56ffa5e230c1a1c8bdf9673bdaa"));
spec.disableShadowBCF();
executeTest(" testAlleleSpecificAnnotations", spec);
}

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
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@ -277,7 +277,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations() throws Exception {
final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard -V "
+ privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("f06d60332cd46036813f652de6d807c9"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("cbb2571eeb95e661acee8f9e1d1cbfbd"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations", spec);
}

4
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
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@ -565,7 +565,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "NA12878.AS.chr20snippet.g.vcf -V " + privateTestDir + "NA12891.AS.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("69b5d245a7411ab45e6bd211cc09a53d"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("f62ae282ec8e32f6104ef84237b8a5a4"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations", spec);
}
@ -575,7 +575,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
public void testAlleleSpecificAnnotations_oneSample() {
final String cmd = "-T GenotypeGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -G Standard -G AS_Standard --disableDithering -V "
+ privateTestDir + "NA12878.AS.chr20snippet.g.vcf";
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("14ecc30b631afce3e3029484c9ee7b92"));
final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("1eefb0ed407b9071f09f9189c9ad45cf"));
spec.disableShadowBCF();
executeTest("testAlleleSpecificAnnotations", spec);
}