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Uncomment code to add deleted bases covering an indel to per-sample genotype reporting, update integration tests accordingly

This commit is contained in:
Guillermo del Angel 2011-09-10 19:41:01 -04:00
parent b399424a9c
commit 9344938360
2 changed files with 13 additions and 13 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -449,7 +449,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
protected int getFilteredDepth(ReadBackedPileup pileup) {
int count = 0;
for ( PileupElement p : pileup ) {
if (/*p.isDeletion() ||*/ BaseUtils.isRegularBase(p.getBase()) )
if (p.isDeletion() || BaseUtils.isRegularBase(p.getBase()) )
count++;
}

24
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -29,7 +29,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("4bd3e874d071c4df250dce32cf441aab"));
Arrays.asList("e6639ea2dc81635c706e6c35921406d7"));
executeTest("test MultiSample Pilot1", spec);
}
@ -50,7 +50,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("82d469145c174486ccc494884852cc58"));
Arrays.asList("d1cbd1fb9f3f7323941a95bc2def7e5a"));
executeTest("test SingleSample Pilot2", spec);
}
@ -60,7 +60,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
//
// --------------------------------------------------------------------------------------------------------------
private final static String COMPRESSED_OUTPUT_MD5 = "a5a9f38c645d6004d4640765a8b77ce4";
private final static String COMPRESSED_OUTPUT_MD5 = "2732b169cdccb21eb3ea00429619de79";
@Test
public void testCompressedOutput() {
@ -81,7 +81,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
// Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
String md5 = "0a45761c0e557d9c2080eb9e7f4f6c41";
String md5 = "cbac3960bbcb9d6192c57549208c182c";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@ -160,8 +160,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testHeterozyosity() {
HashMap<Double, String> e = new HashMap<Double, String>();
e.put( 0.01, "af5199fbc0853cf5888acdcc88f012bc" );
e.put( 1.0 / 1850, "4e6938645ccde1fdf204ffbf4e88170f" );
e.put( 0.01, "aed69402ddffe7f2ed5ca98563bfba02" );
e.put( 1.0 / 1850, "fa94a059f08c1821b721335d93ed2ea5" );
for ( Map.Entry<Double, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -185,7 +185,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("213ebaaaacf850312d885e918eb33500"));
Arrays.asList("1c080e6596d4c830bb5d147b04e2a82c"));
executeTest(String.format("test multiple technologies"), spec);
}
@ -204,7 +204,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -L 1:10,000,000-10,100,000" +
" -baq CALCULATE_AS_NECESSARY",
1,
Arrays.asList("3aecba34a89f3525afa57a38dc20e6cd"));
Arrays.asList("9129ad748ca3be2d3b321d2d7e83ae5b"));
executeTest(String.format("test calling with BAQ"), spec);
}
@ -223,7 +223,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("043973c719a85de29a35a33a674616fb"));
Arrays.asList("0bece77ce6bc447438ef9b2921b2dc41"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -238,7 +238,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -minIndelCnt 1" +
" -L 1:10,000,000-10,100,000",
1,
Arrays.asList("68d4e6c1849e892467aed61c33e7bf24"));
Arrays.asList("5fe98ee853586dc9db58f0bc97daea63"));
executeTest(String.format("test indel caller in SLX witn low min allele count"), spec);
}
@ -251,7 +251,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("f86d453c5d2d2f33fb28ae2050658a5e"));
Arrays.asList("790b1a1d6ab79eee8c24812bb8ca6fae"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}
@ -280,7 +280,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec4 = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "ALL.wgs.union_v2_chr20_100_110K.20101123.indels.sites.vcf -I " + validationDataLocation +
"phase1_GBR_realigned.chr20.100K-110K.bam -o %s -L 20:100,000-110,000", 1,
Arrays.asList("b6c3f771e8844a64681187ebb2b620f1"));
Arrays.asList("4be308fd9e8167ebee677f62a7a753b7"));
executeTest("test MultiSample 1000G Phase1 indels with complicated records emitting all sites", spec4);
}