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Updating MD5s for updated BAM with read groups

This commit is contained in:
Mark DePristo 2011-10-06 12:15:48 -07:00
parent c528233578
commit 6d9c210460
1 changed files with 13 additions and 14 deletions
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27
public/java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java
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@ -36,7 +36,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-R " + hg18Reference +
" -T ClipReads " +
"-I " + validationDataLocation + "clippingReadsTest.bam " +
"-I " + validationDataLocation + "clippingReadsTest.withRG.bam " +
"-os %s " +
"-o %s " + args,
2, // just one output file
@ -46,23 +46,22 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
}
final static String Q10ClipOutput = "b29c5bc1cb9006ed9306d826a11d444f";
@Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "4deca83d80dfa3f093e0dc27d27d1352"); }
@Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1e123233ebd2f35ac3f41b1b7d2c8199"); }
@Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1e123233ebd2f35ac3f41b1b7d2c8199"); }
@Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "b950538d2d8fac1bcee11850c452bd6a"); }
@Test public void testQClip30() { testClipper("clipQSum30", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "b950538d2d8fac1bcee11850c452bd6a"); }
@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 testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "9f70540b795f227668dcf78edcb35c09"); }
@Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "a22347a741640fc6df92700e0e8d6f61"); }
@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 testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "f49e9e61a44115e2be59330259966f53"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + validationDataLocation + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "5c977f261442ab6122d5198fa4086e67"); }
@Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "b89459f373e40f0b835c1faff2208839"); }
@Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + validationDataLocation + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "24e19116ef16a37a6d095ed5c22c2466"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + validationDataLocation + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "38d5f33d198aeee7eebec9feb7b11199"); }
@Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + validationDataLocation + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "ad8d30300cb43d5e300fcc4d2450da8e"); }
@Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1e123233ebd2f35ac3f41b1b7d2c8199"); }
@Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "d44cab2e3b70f5492a0f5b59f0b80043"); }
@Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "b86374a7e6f59e3dd35781e9e8006702"); }
@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 testUseOriginalQuals() {