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Merge pull request #163 from broadinstitute/mc_hmm_caching_again 

Fix another caching issue with the PairHMM
This commit is contained in:
Mark DePristo 2013-04-12 12:34:49 -07:00
parent e5b9b6041c 403f9de122
commit b32457be8d
3 changed files with 11 additions and 11 deletions
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6
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "490ecf6619740c01c81a463392ef23cf");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "7a035437f145b714cb844666b0736925");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"125e93deeb3b390a14d9b777aa2a220f");
"aacfcc50c9aa5cfbec8ae8026d937ecd");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"6957fd0e8a5bc66d2572a6ca8626fa7a");
"eae75a3dc5c2e0fbdf016dbbafe425e2");
}
}

14
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -80,12 +80,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "6fa37c449a800bcd59069be03ad2fff2");
HCTest(CEUTRIO_BAM, "", "c8598545d1c76b470a7784e6b5c2ad4a");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "6140447b34bd1d08b3ed4d473d2c2f23");
HCTest(NA12878_BAM, "", "0b2ca4482e92b9606be904cc25ba0988");
}
@Test(enabled = false) // can't annotate the rsID's yet
@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"cbd119f3d37a9af0b3539c13b8053bd9");
"d00a604abe02586f803b1bb9d63af0f7");
}
@Test
@ -112,7 +112,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "9eeeada2f7145adfe08f538aad704982");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "1eab0eb7a184d981b021a249c3bd0401");
}
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
@ -149,7 +149,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerNearbySmallIntervals() {
HCTestNearbySmallIntervals(NA12878_BAM, "", "16ecd2f282bcb10dc32e7f3fe714a000");
HCTestNearbySmallIntervals(NA12878_BAM, "", "6ab938dede6838c983f84225d4103852");
}
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
@ -166,7 +166,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("b6fd839641ee038048626fbd1154f173"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("e8466846ca420bcbcd52b97f7a661aa3"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -188,7 +188,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("020b1a4feb82f050894f6066dc07cc4a"));
Arrays.asList("8a62597f2c005f373efbe398ab51a2f1"));
executeTest("HC calling on a ReducedRead BAM", spec);
}

2
public/java/src/org/broadinstitute/sting/utils/pairhmm/PairHMM.java
View File

@ -134,7 +134,7 @@ public abstract class PairHMM {
paddedReadLength = readBases.length + 1;
paddedHaplotypeLength = haplotypeBases.length + 1;
final int hapStartIndex = (previousHaplotypeBases == null || haplotypeBases.length != previousHaplotypeBases.length ) ? 0 : findFirstPositionWhereHaplotypesDiffer(haplotypeBases, previousHaplotypeBases);
final int hapStartIndex = (previousHaplotypeBases == null || haplotypeBases.length != previousHaplotypeBases.length || recacheReadValues) ? 0 : findFirstPositionWhereHaplotypesDiffer(haplotypeBases, previousHaplotypeBases);
double result = subComputeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals, insertionGOP, deletionGOP, overallGCP, hapStartIndex, recacheReadValues);