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Update general ploidy md5's due to bad merge of md5's in previous commit, and new shortened interval definition for EMIT_ALL_CONFIDENT_SITES was buggy

This commit is contained in:
Guillermo del Angel 2012-09-18 20:12:15 -04:00
parent ccc3f4ff8d
commit bebd5c14b8
2 changed files with 10 additions and 10 deletions
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1
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java
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@ -200,7 +200,6 @@ public class GeneralPloidyExactAFCalculationModel extends AlleleFrequencyCalcula
combinedPloidy = ploidyPerPool + combinedPloidy; // total number of chromosomes in combinedLikelihoods
}
int k=0;
}
public static CombinedPoolLikelihoods fastCombineMultiallelicPool(final CombinedPoolLikelihoods originalPool, double[] newGL, int originalPloidy, int newGLPloidy, int numAlleles,

19
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java
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@ -20,7 +20,7 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
final String REFSAMPLE_NAME = "NA12878";
final String MTINTERVALS = "MT:1-1000";
final String LSVINTERVALS = "20:40,500,000-41,000,000";
final String LSVINTERVALS_SHORT = "20:40,500,000-41,501,000";
final String LSVINTERVALS_SHORT = "20:40,500,000-40,501,000";
final String NA12891_CALLS = comparisonDataLocation + "Unvalidated/mtDNA/NA12891.snp.vcf";
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";
@ -53,28 +53,29 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
executeTest("testPoolCaller:"+name+" args=" + args, spec);
}
@Test(enabled = true)
public void testSNP_ACS_Pools() {
PC_LSV_Test_short(" -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES","LSV_SNP_ACS","SNP","ec19f0b7c7d57493cecfff988a4815c8");
}
@Test(enabled = true)
public void testBOTH_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","54241500a8ce7df4bedab6e29099dba5");
PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","a636ae291a27843107294f3e7940b98a");
}
@Test(enabled = true)
public void testINDEL_GGA_Pools() {
PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","5515c6b4249505f78eb54140725e3f72");
}
@Test(enabled = true)
public void testSNP_ACS_Pools() {
PC_LSV_Test(" -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES","LSV_SNP_ACS","SNP","90af837f372e3d5143af30bf5c8c2b75");
PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","738fa68a3fc838b4bbad5c257f3e96fe");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","38599f7650a44c5ed7bdd19865483b99");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9bcf1f2c204a251ee2b0b6f17ed59a61");
}
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","789a54438553179b9abec1fbe4df754c");
PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","c73678eeaad574af9ed45045074828fa");
}
@Test(enabled = true)