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Change HashMap to LinkedHashMap for predictable iteration

This commit is contained in:
Ron Levine 2016-04-08 18:45:25 -04:00
parent 2baa7a0b9e
commit 0eba8822e2
3 changed files with 17 additions and 17 deletions
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2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java
View File

@ -158,7 +158,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
*/
@Test
public void testContaminationCorrection() {
M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "d7947ddf0240fe06a44621312831f44c");
M2Test(CCLE_MICRO_TUMOR_BAM, CCLE_MICRO_NORMAL_BAM, CCLE_MICRO_INTERVALS_FILE, "-contamination 0.1", "1df41f2dd6d4715ae1b423bf295ec7c5");
}
/**

30
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -111,18 +111,18 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "", "b86311f6a0b4b5f2cfd05662f03fbe6c");
HCTest(CEUTRIO_BAM, "", "5d9b06d7bf88bb18aa3e8fa6322dff89");
}
@Test
public void testHaplotypeCallerSingleSample() throws IOException {
HCTest(NA12878_BAM, "", "1ceedd80a36e042a93d60e25b94c0b03");
HCTest(NA12878_BAM, "", "b35ba8b7ec8ddfe8268b82e77709c9ca");
}
@Test
public void testHaplotypeCallerMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-ploidy 1", "a7e83df05d8ef3558fa98e8c6a86e12d");
HCTest(CEUTRIO_BAM, "-ploidy 1", "84bd5a2ac22aa47b4436ecaf656b73b1");
}
@Test
@ -132,12 +132,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleTetraploid() throws IOException {
HCTest(NA12878_BAM, "-ploidy 4", "ae463cceb8cb0937440cfe5b56904feb");
HCTest(NA12878_BAM, "-ploidy 4", "894b56fa3afd35e240a7db394da7b4ef");
}
@Test
public void testHaplotypeCallerMinBaseQuality() throws IOException {
HCTest(NA12878_BAM, "-mbq 15", "1ceedd80a36e042a93d60e25b94c0b03");
HCTest(NA12878_BAM, "-mbq 15", "b35ba8b7ec8ddfe8268b82e77709c9ca");
}
@Test
@ -147,46 +147,46 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMinBaseQualityTetraploid() throws IOException {
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "ae463cceb8cb0937440cfe5b56904feb");
HCTest(NA12878_BAM, "-mbq 15 -ploidy 4", "894b56fa3afd35e240a7db394da7b4ef");
}
@Test
public void testHaplotypeCallerGraphBasedSingleSample() throws IOException {
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "58abaabab25b9a75aaf17ab48478f42a");
HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "94dc1ca52ebe24ab118b13558e667253");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSampleHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "d7c7ff3883e8a50be38ec32b1a8fa5b4");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased -ploidy 1", "8aae4fe36d14158ea2cbf5db151f39a1");
}
@Test
public void testHaplotypeCallerGraphBasedMultiSample() throws IOException {
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "ccec6b941d41ac2642450964c3ab85d7");
HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "ea4365e2dd6ae627d6347f2a53ceeaef");
}
@Test
public void testHaplotypeCallerSingleSampleWithDbsnp() throws IOException {
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "48a008f41644c8e4bb256141d095a140");
HCTest(NA12878_BAM, "-D " + b37dbSNP132, "626abc84e03d4488b781cfc5a5f50290");
}
@Test
public void testHaplotypeCallerMultiSampleGGA() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf" +
" -isr INTERSECTION -L " + GGA_INTERVALS_FILE,
"b7d2576ac00c175f4136b2bfbffc4dcd");
"03a9fa3a1c7163c68807d8c713d8040c");
}
@Test
public void testHaplotypeCallerMultiSampleGGAHaploid() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 1 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
"07e0a87e762173bcd6bba5e7af704159");
"6120365c05e74a8e1e1c44d739cbf8cd");
}
@Test
public void testHaplotypeCallerMultiSampleGGATetraploid() throws IOException {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -ploidy 4 -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf -isr INTERSECTION -L 20:10080000-10100000",
"be7315e2866eccfb951ed63090f9119c");
"a3a547a7bf7e488651733da08fd22049");
}
@Test
@ -483,12 +483,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerTandemRepeatAnnotator() throws IOException{
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "abc2daf88b9c5b3c0989f5d06df84ab3");
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A TandemRepeatAnnotator -XA MappingQualityZero -XA SpanningDeletions", "57eed4eec7b49efa1269fd8d58bde718");
}
@Test
public void testHBaseCountsBySample() throws IOException{
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "3e0ee74ec384ae38bda8ac15d8d67cca");
HCTest(NA12878_BAM, " -L 20:10001000-10010000 -A BaseCountsBySample", "5e5d064f2bb90e05e1ab28a087d8469d");
}
}

2
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoods.java
View File

@ -1232,7 +1232,7 @@ public class ReadLikelihoods<A extends Allele> implements SampleList, AlleleList
checkSampleIndex(sampleIndex);
final int alleleCount = alleles.alleleCount();
final int sampleReadCount = readsBySampleIndex[sampleIndex].length;
final Map<A,List<GATKSAMRecord>> result = new HashMap<>(alleleCount);
final Map<A,List<GATKSAMRecord>> result = new LinkedHashMap<>(alleleCount);
for (int a = 0; a < alleleCount; a++)
result.put(alleles.alleleAt(a),new ArrayList<GATKSAMRecord>(sampleReadCount));
readsByBestAlleleMap(sampleIndex,result);