From 2c76f71a03c386091fce5d477a593426bce46337 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 6 Aug 2012 22:48:04 -0400 Subject: [PATCH] Update -maxAlleles argument in integration tests --- ...iedGenotyperGeneralPloidyIntegrationTest.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java index 9b3103274..4d8c6808f 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java @@ -46,33 +46,33 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest { @Test public void testBOTH_GGA_Pools() { - PC_LSV_Test(String.format(" -maxAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","d76e3b910259da819f1e1b2adc68ba8d"); + 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","d76e3b910259da819f1e1b2adc68ba8d"); } @Test public void testINDEL_GGA_Pools() { - PC_LSV_Test(String.format(" -maxAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","ffadcdaee613dab975197bed0fc78da3"); + 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","ffadcdaee613dab975197bed0fc78da3"); } @Test - public void testINDEL_maxAlleles2_ploidy3_Pools_noRef() { - PC_LSV_Test_NoRef(" -maxAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","96087fe9240e3656cc2a4e0ff0174d5b"); + public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() { + PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","96087fe9240e3656cc2a4e0ff0174d5b"); } @Test - public void testINDEL_maxAlleles2_ploidy1_Pools_noRef() { - PC_LSV_Test_NoRef(" -maxAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","6fdae7093831ecfc82a06dd707d62fe9"); + public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() { + PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","6fdae7093831ecfc82a06dd707d62fe9"); } @Test public void testMT_SNP_DISCOVERY_sp4() { - PC_MT_Test(CEUTRIO_BAM, " -maxAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","6b27634214530d379db70391a9cfc2d7"); + PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","6b27634214530d379db70391a9cfc2d7"); } @Test public void testMT_SNP_GGA_sp10() { - PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "e74d4c73ece45d7fb676b99364df4f1a"); + PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "e74d4c73ece45d7fb676b99364df4f1a"); } }