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Updating MD5s 

-- Interval test now uses RG containing BAM
-- DoC sample name ordering has changed.
This commit is contained in:
Mark DePristo 2011-10-04 15:54:45 -07:00
parent a45d985818
commit ffdfdcde3f
2 changed files with 9 additions and 9 deletions
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14
public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
View File

@ -57,11 +57,11 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
// now add the expected files that get generated
spec.addAuxFile("423571e4c05e7934322172654ac6dbb7", baseOutputFile);
spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
spec.addAuxFile("b9a7748e5aec4dc06daed893c901c00d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("229b9b5bc2141c86dbc69c8acc9eba6a", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
spec.addAuxFile("aec669d64d9dd652dd088a5341835ea5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("f6dbd74d32a48abe71ce08d300bce983", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("e3a3467ed259ee3680f8d01980f525b7", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("471c34ad2e4f7228efd20702d5941ba9", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
spec.addAuxFile("9667c77284c2c08e647b162d0e9652d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_statistics"));
spec.addAuxFile("5a96c75f96d6fa6ee617451d731dae37", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_summary"));
spec.addAuxFile("b82846df660f0aac8429aec57c2a62d6", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_counts"));
spec.addAuxFile("d32a8c425fadcc4c048bd8b48d0f61e5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_cumulative_coverage_proportions"));
spec.addAuxFile("7b9d0e93bf5b5313995be7010ef1f528", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics"));
@ -69,10 +69,10 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
spec.addAuxFile("e70952f241eebb9b5448f2e7cb288131", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics"));
spec.addAuxFile("054ed1e184f46d6a170dc9bf6524270c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary"));
spec.addAuxFile("d53431022f7387fe9ac47814ab1fcd88", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
spec.addAuxFile("650ee3714da7fbad7832c9d4ad49eb51", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("a395dafde101971d2b9e5ddb6cd4b7d0", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
spec.addAuxFile("df0ba76e0e6082c0d29fcfd68efc6b77", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
spec.addAuxFile("7dcac2e8962c778081486332a4576dc3", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("a50011571334f17e950ad3ed1149e350", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("e013cb5b11b0321a81c8dbd7c1863787", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
spec.addAuxFile("661160f571def8c323345b5859cfb9da", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
spec.addAuxFile("c95a7a6840334cadd0e520939615c77b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
execute("testBaseOutputNoFiltering",spec);

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

@ -76,7 +76,7 @@ public class IntervalIntegrationTest extends WalkerTest {
// our base file
File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("99c266d777e2e167b8153c858c305fda",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("748a38ed5eb0a043dfc7b82f0d1e8063",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
executeTest("testUnmappedReadInclusion",spec);
@ -97,7 +97,7 @@ public class IntervalIntegrationTest extends WalkerTest {
File baseOutputFile = createTempFile("testUnmappedReadExclusion",".bam");
spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("8236f0b2df5a692e54751b08bc3836fa",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
spec.addAuxFile("651b42456d31ba24e913297b71b32143", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
spec.addAuxFile("b341d808ecc33217f37c0c0cde2a3e2f", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
executeTest("testUnmappedReadExclusion",spec);
}