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Update expected test output for Java 7 

-Changes in Java 7 related to comparators / sorting produce a large number
 of innocuous differences in our test output. Updating expectations now
 that we've moved to using Java 7 internally.

-Also incorporate Eric's fix to the GATKSAMRecordUnitTest to prevent
 intermittent failures.
This commit is contained in:
David Roazen 2013-05-01 15:48:05 -04:00
parent d0980e236a
commit f3c94a3c87
11 changed files with 44 additions and 43 deletions
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12
protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -78,7 +78,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("fbfbd4d13b7ba3d76e8e186902e81378"));
Arrays.asList("42889072698af972f2004ccfe8eae15e"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -86,7 +86,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("19aef8914efc497192f89a9038310ca5"));
Arrays.asList("213560f395280e6a066d0b0497ce8881"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -112,7 +112,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("4f0b8033da18e6cf6e9b8d5d36c21ba2"));
Arrays.asList("7e755bb09169699b76850e76b71a5f5a"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -120,7 +120,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("64ca176d587dfa2b3b9dec9f7999305c"));
Arrays.asList("d8089c5874ff35a7fd7e35ebd7d3b137"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}
@ -128,7 +128,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testExcludeAnnotations() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("f33f417fad98c05d9cd08ffa22943b0f"));
Arrays.asList("e17596007d0db7673d138a9ae4890e82"));
executeTest("test exclude annotations", spec);
}
@ -136,7 +136,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
Arrays.asList("0c810f6c4abef9d9dc5513ca872d3d22"));
Arrays.asList("0ed4c7760f6e7a158b6d743d257300f3"));
executeTest("test overwriting header", spec);
}

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
View File

@ -69,7 +69,7 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
@Test(enabled = true)
public void testBOTH_GGA_Pools() {
executor.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", "71f16e19b7d52e8edee46f4121e59f54");
executor.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", "dac2d7969e109aee9ad2dad573759f58");
}
@Test(enabled = true)
@ -79,6 +79,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "603416111f34e2a735163fa97e1a8272");
executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "66a5a3eb657fac5c621bc0c228ea9caf");
}
}

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
View File

@ -58,16 +58,16 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
@Test(enabled = true)
public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","13de8558acaa0b9082f2df477b45de9b");
executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","9f960977b1b8d90ac75ba4306336553c");
}
@Test(enabled = true)
public void testMT_SNP_DISCOVERY_sp4() {
executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","3fc6f4d458313616727c60e49c0e852b");
executor.PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","296917e690616682b79229ec5f923bdb");
}
@Test(enabled = true)
public void testMT_SNP_GGA_sp10() {
executor.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", "1bebbc0f28bff6fd64736ccca8839df8");
executor.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", "545d85ce79841f01886a5cf824a4a12c");
}
}

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
View File

@ -73,7 +73,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
" -o %s" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("d8b0c5be39ec6b239641c2f2646d2bc3"));
Arrays.asList("ea4c4e020f59f48901d5820c8e4f6001"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -111,7 +111,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("16d975480ff1e689113171805b916b62"));
Arrays.asList("79f7fc64da8f25eda1f1ee139ecdd657"));
executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
}
@ -121,7 +121,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
Arrays.asList("60ed3f8d5bc3f765e6ce3fa698b68bb7"));
Arrays.asList("15508fcf61380a91b6611307f182447b"));
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
}

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
View File

@ -96,7 +96,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testMultipleSNPAlleles() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
Arrays.asList("09a1a4d4bf0289bcc5e8a958f783a989"));
Arrays.asList("21d1d3c6a50006c723cec738f19caeb6"));
executeTest("test Multiple SNP alleles", spec);
}
@ -112,7 +112,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
public void testReverseTrim() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
Arrays.asList("57a1bb44967988f2b7ae7779127990ae"));
Arrays.asList("314b99eb146de1fdafed872ecbe1cfc2"));
executeTest("test reverse trim", spec);
}

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java
View File

@ -74,7 +74,7 @@ public class UnifiedGenotyperReducedReadsIntegrationTest extends WalkerTest {
@Test
public void testReducedBamINDELs() {
testReducedCalling("INDEL", "9a986b98ed014576ce923e07452447f4");
testReducedCalling("INDEL", "19bc6a74250ec19efc4e1b4ee6515ac0");
}

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", "", "27db36467d40c3cde201f5826e959d78");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "0bf5ae740bf9bd14c8d60d7849c45eb3");
}
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",
"ed3b577e6f7d68bba6774a62d9df9cd9");
"5954a46971b7546d30151b068cded42a");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"a594a28d8053c3e969c39de81a9d03d6");
"b3684c670f68f5a3a348a7fd2b25f10a");
}
}

16
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -80,12 +80,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "aeab5f0d40852e6332b96481981a0e46");
HCTest(CEUTRIO_BAM, "", "2e10ab97afd4492c2a153b85871a2c2d");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "18d5671d8454e8a0c05ee5f6e9fabfe3");
HCTest(NA12878_BAM, "", "affed81386dfe60e0b0d4e7e0525918f");
}
@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",
"28c3b1f276ec8198801aafe880e40fb6");
"65188ec4e3b91796f62bfb5b965ccf1f");
}
@Test
@ -112,7 +112,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "bac6f98e910290722df28da44b41f06f");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "125e91ebe43108b2b514c58a9b6d3a4f");
}
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, "", "65e7b1b72a2411d6360138049914aa3a");
HCTestNearbySmallIntervals(NA12878_BAM, "", "2d295ce36066d9d8d9ee9c67e6e2cbd1");
}
// 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 --disableDithering -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("cb190c935541ebb9f660f713a882b922"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("153d2251de7d22f423cd282b1505fbc0"));
executeTest("HCTestStructuralIndels: ", spec);
}
@ -188,7 +188,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void HCTestReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering -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("0df626cd0d76aca8a05a545d0b36bf23"));
Arrays.asList("0c29e4049908ec47a3159dce33d477c3"));
executeTest("HC calling on a ReducedRead BAM", spec);
}
@ -196,7 +196,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testReducedBamWithReadsNotFullySpanningDeletion() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
Arrays.asList("8adfa8a27a312760dab50787da595c57"));
Arrays.asList("3306889b8d0735ce575bee281c1b8846"));
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
}
}

26
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
View File

@ -82,23 +82,23 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
// now add the expected files that get generated
spec.addAuxFile("0f9603eb1ca4a26828e82d8c8f4991f6", baseOutputFile);
spec.addAuxFile("51e6c09a307654f43811af35238fb179", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
spec.addAuxFile("229b9b5bc2141c86dbc69c8acc9eba6a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("520720a88ae7608257af51bc41c06b87", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
spec.addAuxFile("e69ee59f447816c025c09a56e321cef8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("fa054b665d1ae537ada719da7713e11b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("28dec9383b3a323a5ce7d96d62712917", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("6958004a8156f3f267caa6b04cf90f5f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("ebbfc9b9f4e12ac989c127061948c565", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("e003bef6762833a5cebca25d94194616", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("a836b92ac17b8ff9788e2aaa9116b5d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
spec.addAuxFile("d32a8c425fadcc4c048bd8b48d0f61e5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
spec.addAuxFile("0732b6d2db9c94b0fcf18ca1f19772a8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
spec.addAuxFile("4656c8797696cf5ef0cdc5971271236a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("6f1d7f2120a4ac524c6026498f45295a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("69c424bca013159942337b67fdf31ff8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
spec.addAuxFile("3522f7380554b926c71a7258250c1d63", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary"));
spec.addAuxFile("2cd9d8c5e37584edd62ca6938659cf59", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("78fdd35a63a7a4c6b3a043b946b04730", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
spec.addAuxFile("6909d50a7da337cd294828b32b945eb8", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("a395dafde101971d2b9e5ddb6cd4b7d0", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("aa00e3652dd518ccbae2caa00171835b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("185b910e499c08a8b88dd3ed1ac9e8ec", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("d5d11b686689467b5a8836f0a07f447d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("ad1a2775a31b1634daf64e691676bb96", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
spec.addAuxFile("0ce5ebfa46b081820d013bdbbfe42d34", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("c7c5bad6c6818995c634f350aa66fde9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("949c9ce745753cd98f337600d3931d09", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
execute("testBaseOutputNoFiltering",spec);
}
@ -115,7 +115,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("6ccd7d8970ba98cb95fe41636a070c1c",baseOutputFile);
spec.addAuxFile("7d87783b3d98b928cac16d383ceca807",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("4429d33ce8836c09ba2b5ddfae2f998e",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
execute("testNoCoverageDueToFiltering",spec);
}

2
public/java/test/org/broadinstitute/sting/utils/crypt/GATKKeyIntegrationTest.java
View File

@ -130,7 +130,7 @@ public class GATKKeyIntegrationTest extends WalkerTest {
{ "corrupt_bad_isize_field.key", UserException.UnreadableKeyException.class },
{ "corrupt_bad_crc.key", UserException.UnreadableKeyException.class },
{ "corrupt_no_email_address.key", UserException.UnreadableKeyException.class },
{ "corrupt_no_sectional_delimiter.key", UserException.KeySignatureVerificationException.class },
{ "corrupt_no_sectional_delimiter.key", UserException.UnreadableKeyException.class },
{ "corrupt_no_signature.key", UserException.UnreadableKeyException.class },
{ "corrupt_bad_signature.key", UserException.KeySignatureVerificationException.class },
{ "corrupt_non_gzipped_valid_key.key", UserException.UnreadableKeyException.class }

3
public/java/test/org/broadinstitute/sting/utils/sam/GATKSAMRecordUnitTest.java
View File

@ -42,7 +42,7 @@ public class GATKSAMRecordUnitTest extends BaseTest {
GATKSAMRecord read, reducedRead;
final static String BASES = "ACTG";
final static String QUALS = "!+5?";
final private static int[] REDUCED_READ_COUNTS = new int[]{10, 20, 30, 40, 1};
final private static int[] REDUCED_READ_COUNTS = new int[]{10, 20, 30, 40};
@BeforeClass
public void init() {
@ -200,6 +200,7 @@ public class GATKSAMRecordUnitTest extends BaseTest {
@Test
public void testGetReducedCountsIsCorrect() {
reducedRead.setReducedReadCountsTag(REDUCED_READ_COUNTS);
final int[] counts = reducedRead.getReducedReadCounts();
Assert.assertNotSame(counts, reducedRead.getAttribute(GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG));
for ( int i = 0; i < counts.length; i++ )