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Update MD5s to reflect version number change in the BAM header 

I've confirmed via a script that all of these differences only
involve the version number bump in the BAM headers and nothing
else:

< @HD   VN:1.0  GO:none SO:coordinate
---
> @HD   VN:1.4  GO:none SO:coordinate
This commit is contained in:
David Roazen 2013-02-01 12:14:31 -05:00
parent 874913318a
commit 4c0a3b182e
7 changed files with 38 additions and 38 deletions
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8
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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@ -188,12 +188,12 @@ public class BQSRIntegrationTest extends WalkerTest {
public Object[][] createPRTestData() {
List<Object[]> tests = new ArrayList<Object[]>();
tests.add(new Object[]{1, new PRTest(" -qq -1", "b8d296fb78adc5cff7ce12073a69d985")});
tests.add(new Object[]{1, new PRTest(" -qq 6", "2ee0cedf84c1a33a807438172bc36c11")});
tests.add(new Object[]{1, new PRTest(" -DIQ", "46cf74900bf8b13438e6a195b3085c48")});
tests.add(new Object[]{1, new PRTest(" -qq -1", "fcc136b877fbde38791533b0f1ae39e4")});
tests.add(new Object[]{1, new PRTest(" -qq 6", "f21b537c1689b8051b878ea5cc9b61a0")});
tests.add(new Object[]{1, new PRTest(" -DIQ", "1d04a242bf825177d6a45eff9fbed647")});
for ( final int nct : Arrays.asList(1, 2, 4) ) {
tests.add(new Object[]{nct, new PRTest("", "88b88f006ebb1aade85089bfba5a9e8d")});
tests.add(new Object[]{nct, new PRTest("", "b6f343ac69c63cdb49205c13e67297fc")});
}
return tests.toArray(new Object[][]{});

12
protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -60,8 +60,8 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
private static final String baseCommand = baseCommandPrefix + "-o %s ";
private static final String base_md5 = "7574ab7d0b1ee5d44a0b3f85b6e944e6";
private static final String base_md5_with_SW_or_VCF = "a918d69d26d3c87b29002ed31f428c48";
private static final String base_md5 = "a102dd55451799e5f053c784b762087e";
private static final String base_md5_with_SW_or_VCF = "06b8eefcbd785e929027feaa22bb060d";
@Test
public void testDefaults() {
@ -84,7 +84,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
1,
Arrays.asList("36718f10d523dfb0fa2a709480f24bd4"));
Arrays.asList("1b24b0f2a20aed1adc726d1b296a3192"));
executeTest("realigner known indels only from VCF", spec1);
}
@ -101,7 +101,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
public void testLods() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-LOD 60", base_md5 );
e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "9a75a0f7ad0442c78d0f8df260e733a4" );
e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "4bf28d3c0337682d439257874377a681" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -117,7 +117,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",
1,
Arrays.asList("e98f51d71f0a82141b36a7e9f94db237"));
Arrays.asList("f4f6c3b2a2be0306a0ecd3def334bafe"));
executeTest("realigner long run", spec);
}
@ -126,7 +126,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW",
1,
Arrays.asList("58ac675d0699eb236d469b8e84513d11"));
Arrays.asList("71fb521f8febfe2dc683fc636e28ae7d"));
executeTest("realigner no output tags", spec);
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java
View File

@ -43,13 +43,13 @@ public class BAQIntegrationTest extends WalkerTest {
// --------------------------------------------------------------------------------------------------------------
@Test
public void testPrintReadsNoBAQ() {
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("d97340a2bba2c6320d1ebeb86024a27c"));
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF", 1, Arrays.asList("11af64ba020262d06b490bae2c5e08f8"));
executeTest(String.format("testPrintReadsNoBAQ"), spec);
}
@Test
public void testPrintReadsRecalBAQ() {
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("4ac691bde1ba1301a59857694fda6ae2"));
WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE", 1, Arrays.asList("96ec97cf92f1f660bd5244c6b44539b3"));
executeTest(String.format("testPrintReadsRecalBAQ"), spec);
}
}

26
public/java/test/org/broadinstitute/sting/gatk/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", "33e781084379aae538954e30919e8fd3"); }
@Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "57c05b6241db7110148a91fde2d431d0"); }
@Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "57c05b6241db7110148a91fde2d431d0"); }
@Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "67263a39d5127f2660a5b638ff32056a"); }
@Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "12be03c817d94bab88457e5afe74256a"); }
@Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); }
@Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1cfc9da4867765c1e5b5bd6326984634"); }
@Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "0bcfd177fe4be422898eda8e161ebd6c"); }
@Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "764846d0592f346a33525af674fd7a10"); }
@Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "3061cf742f9e5526a61130128ae761a3"); }
@Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "aed836c97c6383dd80e39a093cc25e08"); }
@Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "5f6e08bd44d6faf5b85cde5d4ec1a36f"); }
@Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "b89459f373e40f0b835c1faff2208839"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "24e19116ef16a37a6d095ed5c22c2466"); }
@Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "f3cb42759428df80d06e9789f9f9f762"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "44658c018378467f809b443d047d5778"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "ad8d30300cb43d5e300fcc4d2450da8e"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "bae38f83eb9b63857f5e6e3c6e62f80c"); }
@Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "57c05b6241db7110148a91fde2d431d0"); }
@Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "2a1a3153e0942ab355fd8a6e082b30e0"); }
@Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "50d43d63d8e39f67a87a6359963c6f52"); }
@Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1cfc9da4867765c1e5b5bd6326984634"); }
@Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "3b32da2eaab7a2d4729fdb486cedbb2f"); }
@Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "9d355b0f6d2076178e92bd7fcd8f5adb"); }
@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("22db22749f811d30216215e047461621", "55c01ccc2e84481b22d3632cdb06c8ba"));
Arrays.asList("c83b4e2ade8654a2818fe9d405f07662", "55c01ccc2e84481b22d3632cdb06c8ba"));
executeTest("clipOriginalQuals", spec);
}
}

20
public/java/test/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java
View File

@ -54,17 +54,17 @@ public class PrintReadsIntegrationTest extends WalkerTest {
@DataProvider(name = "PRTest")
public Object[][] createPrintReadsTestData() {
return new Object[][]{
{new PRTest(hg18Reference, "HiSeq.1mb.bam", "", "dc8e5451dd29757c336013146010f73a")},
{new PRTest(hg18Reference, "HiSeq.1mb.bam", " -compress 0", "fde82269c78c9e91e57286433531b4af")},
{new PRTest(hg18Reference, "HiSeq.1mb.bam", " -simplifyBAM", "0531717b32a7e21c0de70b1526b0751f")},
{new PRTest(hg18Reference, "HiSeq.1mb.bam", " -n 10", "cdc4ddf9ee1d2ecf37168da8ef23c270")},
{new PRTest(hg18Reference, "HiSeq.1mb.bam", "", "fa9c66f66299fe5405512ac36ec9d0f2")},
{new PRTest(hg18Reference, "HiSeq.1mb.bam", " -compress 0", "488eb22abc31c6af7cbb1a3d41da1507")},
{new PRTest(hg18Reference, "HiSeq.1mb.bam", " -simplifyBAM", "1510dc4429f3ed49caf96da41e8ed396")},
{new PRTest(hg18Reference, "HiSeq.1mb.bam", " -n 10", "0e3d1748ad1cb523e3295cab9d09d8fc")},
// See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance()
{new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", "", "0a9ce949d07a84cb33a1a8e3358bf679")},
{new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1", "6e920b8505e7e95d67634b0905237dbc")},
{new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L unmapped", "13bb9a91b1d4dd2425f73302b8a1ac1c")},
{new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1 -L unmapped", "6e920b8505e7e95d67634b0905237dbc")},
{new PRTest(b37KGReference, "oneReadAllInsertion.bam", "", "6caec4f8a25befb6aba562955401af93")},
{new PRTest(b37KGReference, "NA12878.1_10mb_2_10mb.bam", "", "c43380ac39b98853af457b90e52f8427")}
{new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", "", "e1cac555f3d720f611c47eec93e84bd9")},
{new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1", "6e2558317d409195eab3006dc9e5524c")},
{new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L unmapped", "2d32440e47e8d9d329902fe573ad94ce")},
{new PRTest(b37KGReference, "unmappedFlagReadsInLastLinearBin.bam", " -L 1 -L unmapped", "6e2558317d409195eab3006dc9e5524c")},
{new PRTest(b37KGReference, "oneReadAllInsertion.bam", "", "349650b6aa9e574b48a2a62627f37c7d")},
{new PRTest(b37KGReference, "NA12878.1_10mb_2_10mb.bam", "", "0c1cbe67296637a85e80e7a182f828ab")}
};
}

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

@ -38,7 +38,7 @@ public class GATKKeyIntegrationTest extends WalkerTest {
public static final String BASE_COMMAND = String.format("-T PrintReads -R %s -I %s -o %%s",
publicTestDir + "exampleFASTA.fasta",
publicTestDir + "exampleBAM.bam");
public static final String MD5_UPON_SUCCESSFUL_RUN = "b9dc5bf6753ca2819e70b056eaf61258";
public static final String MD5_UPON_SUCCESSFUL_RUN = "e7b4a5b62f9d4badef1cd07040011b2b";
private void runGATKKeyTest ( String testName, String etArg, String keyArg, Class expectedException, String md5 ) {

4
public/java/test/org/broadinstitute/sting/utils/interval/IntervalIntegrationTest.java
View File

@ -78,7 +78,7 @@ public class IntervalIntegrationTest extends WalkerTest {
// our base file
File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("748a38ed5eb0a043dfc7b82f0d1e8063",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("95e98192e5b90cf80eaa87a4ace263da",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
executeTest("testUnmappedReadInclusion",spec);
@ -99,7 +99,7 @@ public class IntervalIntegrationTest extends WalkerTest {
// our base file
File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("083ef1e9ded868e0d12c05a1354c0319",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("3944b5a6bfc06277ed3afb928a20d588",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
executeTest("testUnmappedReadInclusion",spec);