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Change to GKL 0.5.5, which fixes a bug in FPGA 'private' mode (#1623) 

Update GKL to version 0.5.5, which fixes a bug in FPGA 'private' mode. Integration test results were updated to reflect different fallback behavior when AVX is not available.
This commit is contained in:
Ernesto Brau 2017-08-18 22:51:33 -04:00 committed by Geraldine Van der Auwera
parent 3c841eaab5
commit aa8b2ab535
13 changed files with 66 additions and 66 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
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@ -198,13 +198,13 @@ public class BQSRIntegrationTest extends WalkerTest {
public Object[][] createPRTestData() {
List<Object[]> tests = new ArrayList<Object[]>();
tests.add(new Object[]{1, new PRTest(" -qq -1", "8a38828e3b14ce067614d4248e3ea95a")});
tests.add(new Object[]{1, new PRTest(" -qq 6", "e4f23250b2c87f0d68d042cc3d2ec1d3")});
tests.add(new Object[]{1, new PRTest(" -DIQ", "2dfa45f004d3a371fd290ed67fbdf573")});
tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30", "4882354d9e603f9bbe7c9591bba0a573")});
tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30 -RDQ", "6ffdfc4593e83f7c234b6249412433af")});
tests.add(new Object[]{1, new PRTest(" -qq -1", "e9969c6d7fd35d96b82c691b4ced5443")});
tests.add(new Object[]{1, new PRTest(" -qq 6", "b4b271acac003b8504b530c5526d43ad")});
tests.add(new Object[]{1, new PRTest(" -DIQ", "ec795d16746c3bdf5e54c57337e6eed6")});
tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30", "d50df5a7bcc8f195479f64285c124d18")});
tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30 -RDQ", "58b9df85e49eb3ee228f0d581c168791")});
for ( final int nct : Arrays.asList(1, 2, 4) ) {
tests.add(new Object[]{nct, new PRTest("", "6451093cadfc14d7359617b2a7ea6db8")});
tests.add(new Object[]{nct, new PRTest("", "f4704ba2894ec0aec8a55ce6b361f768")});
}
return tests.toArray(new Object[][]{});

2
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java
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@ -138,7 +138,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
public void testTruePositivesDream3TrackedDropped() {
M2TestWithDroppedReads(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, "21:10935369", "",
"48a446d47bb10434cb7f0ee726d15721",
"6ecaeb74893249dfa5723b2266c957e2");
"265a72d3f79bb0fe054a847ab0c01c67");
}
/**

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -133,7 +133,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeBAMOutFlags() throws IOException {
final String md5BAMOut = "69aae17f8cd384666ec7c3c1f3d3eb57";
final String md5BAMOut = "0934466fa2b8648af9e6267286a57151";
HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "df622103b0a6917f2299b1acfd0ed0ac", md5BAMOut);
validateForwardedProgramRecords(new ArrayList<>(Arrays.asList(new File(NA12878_BAM))), md5BAMOut);
}
@ -330,7 +330,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testLeftAlignmentBamOutBugFix() throws IOException {
final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
final String md5BAMOut = "27e729df3b166c81792a62a5b57ef7b3";
final String md5BAMOut = "60db3996cd37a863d8b93218fcbf1c8b";
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
+ " --no_cmdline_in_header -bamout %s -o " + outputVCF + " -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(md5BAMOut));
@ -541,7 +541,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
public void testHaplotypeCallerReadPosRankSum() throws IOException {
final File testBAM = new File(privateTestDir + "testReadPos.snippet.bam");
final String md5Variants = "e664b7a9da71cf81e14648ac7e698eea";
final String md5BAMOut = "3ef35732e49980093ad445e3ac5731fa";
final String md5BAMOut = "74f2cab2d2d0d999b54456b73e597d6c";
final String base = String.format("-T HaplotypeCaller -R %s -I %s -L 1:3753063 -ip 100 ", REF, testBAM) +
" --no_cmdline_in_header -o %s -bamout %s";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5Variants, md5BAMOut));

10
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java
View File

@ -87,7 +87,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsWithOverhangs() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
Arrays.asList("72fbeb2043f005e1698e21563f0625a9"));
Arrays.asList("b721d997bd09873a244fee97c1e58af1"));
executeTest("test splits with overhangs", spec);
}
@ -95,7 +95,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsFixNDN() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "splitNCigarReadsSnippet.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS -fixNDN", 1,
Arrays.asList("add7012d5e814d6cfd32f6cac1eb8ce3"));
Arrays.asList("9aa80944c2c7ee8a1f259907e3d8b51c"));
executeTest("test fix NDN", spec);
}
@ -103,7 +103,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsWithOverhangsNotClipping() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads --doNotFixOverhangs -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
Arrays.asList("6a55ac0a945e010bf03e1dd8f7749417"));
Arrays.asList("4134e1ff0eaaa9986e19526a7c3a8319"));
executeTest("test splits with overhangs not clipping", spec);
}
@ -111,7 +111,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsWithOverhangs0Mismatches() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads --maxMismatchesInOverhang 0 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
Arrays.asList("8a577047955ff9edca3caf1f6e545d3e"));
Arrays.asList("94ebc9fbd64684e50c5f54ad5ff042b6"));
executeTest("test splits with overhangs 0 mismatches", spec);
}
@ -119,7 +119,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
public void testSplitsWithOverhangs5BasesInOverhang() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T SplitNCigarReads --maxBasesInOverhang 5 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
Arrays.asList("bdd822868b88063cf50c6336ed1a5e64"));
Arrays.asList("b737b2dfb22a608ee3def6137fed9414"));
executeTest("test splits with overhangs 5 bases in overhang", spec);
}
}

14
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java
View File

@ -64,7 +64,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
1,
Arrays.asList("d929369b9095420a8aaff2595ec2f80a"));
Arrays.asList("b5680f835aff1da6e1e60123d39f2371"));
executeTest("testVariants", spec);
}
@ -74,7 +74,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-RL 70 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
1,
Arrays.asList("bbc65e4f8bd3a1656616476a1e190ecf"));
Arrays.asList("177d32e0b13bd40aaeef71e8e5ffefe7"));
executeTest("testReadLength", spec);
}
@ -84,7 +84,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-ER 40 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
1,
Arrays.asList("cb0e4b11bbd1b5a154ad6c99541cd017"));
Arrays.asList("7353b4d148221f4f4975f07712413e18"));
executeTest("testErrorRate", spec);
}
@ -94,7 +94,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-RGPL SOLID -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
1,
Arrays.asList("2b5c6cda9a434c9e25e5da5599eeae51"));
Arrays.asList("6f7a2ff3aa3c2e24a00f04dc770a4140"));
executeTest("testPlatformTag", spec);
}
@ -105,7 +105,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SimulateReadsForVariants --no_pg_tag --useAFAsAlleleFraction -DP 100 -R " + b37KGReference + " -V " + publicTestDir + "forAlleleFractionSimulation.vcf -o %s",
1,
Arrays.asList("1ae2c354718b470e30b44d5e59cb9944"));
Arrays.asList("f19d4b62269512fff0dcce21874c0d43"));
executeTest("testAlleleFraction", spec);
}
@ -116,7 +116,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s",
1,
Arrays.asList("5c069bff8efb988660c7f6d28a3117fc"));
Arrays.asList("052f1b644848cfd058cd2aeb0b6f2fd2"));
executeTest("testLongInsertFailure", spec);
}
@ -126,7 +126,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-RL 269 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s",
1,
Arrays.asList("0657f6a692d22b5e2b7f5832710042e4"));
Arrays.asList("33f7da2e0b711a9ad28cb49c60e648be"));
executeTest("testLongInsertSuccess", spec);
}

8
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
View File

@ -324,12 +324,12 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
@Test()
public void testDefaultBaseQualities20() {
executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "90a450f74554bbd2cc3a9e0f9de68e26"));
executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "da5a4293e125f00ecbdfd450b80d8357"));
}
@Test()
public void testDefaultBaseQualities30() {
executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "ec11db4173ce3b8e43997f00dab5ae26"));
executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "c82e72ee08d545266927a7f2e8ab24c3"));
}
@Test(expectedExceptions = Exception.class)
@ -732,10 +732,10 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
public void testSAMWriterFeatures() {
testBAMFeatures("-compress 0", "49228d4f5b14c4cfed4a09372eb71139");
testBAMFeatures("-compress 9", "bc61a1b2b53a2ec7c63b533fa2f8701b");
testBAMFeatures("-simplifyBAM", "a1127bab46674b165496b79bb9fa7964");
testBAMFeatures("-simplifyBAM", "f66b671b32d1bbbf65a88585a64b556a");
//Validate MD5
final String expectedMD5 = "c58b9114fc15b53655f2c03c819c29fd";
final String expectedMD5 = "a0c0f1fafc248ac82a84b8ca71292caf";
final File md5Target = testBAMFeatures("--generate_md5", expectedMD5);
final File md5File = new File(md5Target.getAbsoluteFile() + ".md5");
md5File.deleteOnExit();

8
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java
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@ -41,16 +41,16 @@ public class CramIntegrationTest extends WalkerTest {
return new Object[][] {
{"PrintReads", "exampleBAM.bam", "", "cram", ""}, // Bypass MD5 check since the CRAM header stores the file name
{"PrintReads", "exampleCRAM.cram", "", "cram", ""},
{"PrintReads", "exampleCRAM.cram", "", "bam", "e7834d5992a69143d7c463275213bbf8"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "d362fbf30a2c77a2653f1c8eb2dd8fc1"},
{"PrintReads", "exampleCRAM.cram", "", "bam", "50c55e1040aa0ffd4036aa581fcfe8af"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "f74f78bd16aed8a395f0e79e3898ab19"},
{"CountLoci", "exampleCRAM.cram", "", "txt", "ade93df31a6150321c1067e749cae9be"},
{"CountLoci", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
{"CountReads", "exampleCRAM.cram", "", "txt", "4fbafd6948b6529caa2b78e476359875"},
{"CountReads", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "a11bd125b69f651aaa2ae68c8ccab22f"},
{"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "1a6331f0e7afdccd07425df251d28811"},
{"CountLoci", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
{"CountReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
{"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "9e3e8b5a58dfcb50f5b270547c01d56a"},
{"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "41f8ebb256120befc6ea7d228915b349"},
{"CountLoci", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
{"CountReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
};

6
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
View File

@ -62,7 +62,7 @@ public class IntervalIntegrationTest extends WalkerTest {
// our base file
File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("c66bb2c3c5382e2acff09b2b359562bb",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("4eeb9b07d3c9ddd4ea9eada7805903a2",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
executeTest("testUnmappedReadInclusion",spec);
@ -109,8 +109,8 @@ public class IntervalIntegrationTest extends WalkerTest {
// our base file
File baseOutputFile = createTempFile("testMixedMappedAndUnmapped",".bam");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("c64cff3ed376bc8f2977078dbdac4518",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
spec.addAuxFile("70ac0317c0c13d885e6c2de4f837cdd3",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("df469db01610ddb731868dfb28917142", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
executeTest("testMixedMappedAndUnmapped",spec);
}

2
public/gatk-root/pom.xml
View File

@ -89,7 +89,7 @@
<dependency>
<groupId>com.intel.gkl</groupId>
<artifactId>gkl</artifactId>
<version>0.5.2</version>
<version>0.5.5</version>
</dependency>
<dependency>
<groupId>log4j</groupId>

4
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java
View File

@ -44,13 +44,13 @@ public class BAQIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
@Test
public void testPrintReadsNoBAQ() {
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("e33187ca383c7f5c75c5d547ec79e1cb"));
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("526dbbb390dbd36daa70ac35a8eddc36"));
executeTest(String.format("testPrintReadsNoBAQ"), spec);
}
@Test
public void testPrintReadsRecalBAQ() {
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("a25043edfbfa4f21a13cc21064b460df"));
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("25cb8f91e31a07cca2e141a119c9e020"));
executeTest(String.format("testPrintReadsRecalBAQ"), spec);
}
}

26
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java
View File

@ -47,22 +47,22 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
}
final static String Q10ClipOutput = "b29c5bc1cb9006ed9306d826a11d444f";
@Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "bcf0d1e13537f764f006ef6d9b401ea7"); }
@Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
@Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "27847d330b962e60650df23b6efc8c3c"); }
@Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "f89ec5439e88f5a75433150da0069034"); }
@Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "2e617e0f0b4a1bf45dbb666da0a6a16c"); }
@Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
@Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
@Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "3a9a10966cce58baf9e9400a2c5f99ca"); }
@Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "987007f6e430cad4cb4a8d1cc1f45d91"); }
@Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "ec4cf54ed50a6baf69dbf98782c19aeb"); }
@Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "701f03388ffaeb0f92be1e719e2477df"); }
@Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "7dc5da735c437b6523e0823a1ed0e981"); }
@Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "a9cf540e4ed2514061248a878e09a09c"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "906871df304dd966682e5798d59fc86b"); }
@Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "daa41acd8c9f1a75c8107d0fd0db8cf0"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "b1812de69c967059362139a269044362"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "b41995fea04034ca0427c4a71504ef83"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "9f999ed70684fdfb8dba019ff71741fe"); }
@Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
@Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "195b8bdfc0186fdca742764aa9b06363"); }
@Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "08d16051be0b3fa3453eb1e6ca48b098"); }
@Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
@Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "b7ce95f277d5f66b7f5a60ffbf9692cf"); }
@Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "55c9d86c18c5a59a98429e8a5076e871"); }
@Test
public void testUseOriginalQuals() {
@ -74,7 +74,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
" -OQ -QT 4 -CR WRITE_Q0S" +
" -o %s -os %s",
2,
Arrays.asList("a2819d54b2110150e38511f5a55db91d", "55c01ccc2e84481b22d3632cdb06c8ba"));
Arrays.asList("0e4c116fa07c3d8190eefe6968a0b819", "55c01ccc2e84481b22d3632cdb06c8ba"));
executeTest("clipOriginalQuals", spec);
}
}

28
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java
View File

@ -59,27 +59,27 @@ public class PrintReadsIntegrationTest extends WalkerTest {
@DataProvider(name = "PRTest")
public Object[][] createPrintReadsTestData() {
return new Object[][]{
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "0aa3505ba61e05663e629011dd54e423")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "83d1454dc01cd2e7458dad4012695f64")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -compress 0", "0aec10d19e0dbdfe1d0cbb3eddaf623a")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "c565d9cd4838a313e7bdb30530c0cf71")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "917440a38aba707ec0e012168590981a")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "60255a68df1b8f2fbba373d75274f0de")},
{new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "eb7c6bacca5fee09b8df50880eb81ee6")},
// See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance()
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "0b58c903f54e8543a8b2ce1439aa769b")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "5b1154cc81dba6bcfe76188e4df8d79c")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "a84efdc3d4a8d6329b5f0b494dd280d2")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")},
{new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "", "e212d1799ae797e781b17e630656a9a1")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "", "0387c61303140d8899fcbfdd3e72ed80")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "3d67c398ce2ac1deeddbccbd850380a7")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "37cdd8871843693f2650d7b48c8ae1d4")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "4d63fd6e977a53e5d9590bd030b40bd0")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "a834400e3bd69045eb8a9e94131633f5")},
{new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "37cdd8871843693f2650d7b48c8ae1d4")},
{new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "", "6c04aac25e2136fee395897aac96bea8")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "", "57a9bc1f7dd4e7717ee796c484bcf45a")},
// Tests for filtering options
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
"", "ad56da66be0bdab5a8992de9617ae6a5")},
"", "e691d61df10f7614d73c8ecb46c75ee1")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
" -readGroup SRR359098", "c3bfe28722a665e666098dbb7048a9f1")},
" -readGroup SRR359098", "7644eab114bf537411218f782d75a6a6")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
" -readGroup 20FUK.3 -sn NA12878", "8191f8d635d00b1f4d0993b785cc46c5")},
" -readGroup 20FUK.3 -sn NA12878", "351d5da29874033e50d29c5c36575a6c")},
{new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
" -sn na12878", "92a85b4223ec45e114f12a1fe6ebbaeb")},
" -sn na12878", "9056d852418dd2083f38e3eac1551fcd")},
};
}

6
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java
View File

@ -43,9 +43,9 @@ public class SplitSamFileIntegrationTest extends WalkerTest {
" --outputRoot " + prefix,
Collections.<String>emptyList()
);
addSplitOutput(spec, prefix, "NA12878", "3e28b666fb673be138eca9bd3db9520b");
addSplitOutput(spec, prefix, "NA12891", "af01069bc3da4252ce8417a03d11f48b");
addSplitOutput(spec, prefix, "NA12892", "cfa1cb6aaca03900160bd5627f4f698b");
addSplitOutput(spec, prefix, "NA12878", "356bddf614a44a0234f7b116f5cde998");
addSplitOutput(spec, prefix, "NA12891", "5dd92a0089e3f781e77d94010264b9fd");
addSplitOutput(spec, prefix, "NA12892", "ea8f16c18c89b49ce9d32d76c6af75f9");
executeTest("testSplitSamFile", spec);
}