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Surprisingly, the TileCovariate was indeed covered in integration tests. Updated. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5997 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-06-14 17:40:23 +00:00
parent 6f7c4d1142
commit 5be4f31515
1 changed files with 6 additions and 7 deletions
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13
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
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@ -18,10 +18,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariates1() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "3faa38f5363131bb30504c8980d2997b" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "b12f7eb32b845796fd5b66884a9f37b1");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "66a184983af42390d8c20878111acf5a" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "286ebc7d8245d47e7d11e92e63800fff" );
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "7b5832d4b2a23b8ef2bb639eb59bfa88" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "f4f8a49bb5764d2a8f61e055f64dcce4");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "e6f7b4ab9aa291022e0ba8b7dbe4c77e" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "570506533f079d738d70934dfe1c02cd" );
for ( String parallelism : Arrays.asList("", " -nt 4")) {
for ( Map.Entry<String, String> entry : e.entrySet() ) {
@ -39,7 +39,6 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
" -cov QualityScoreCovariate" +
" -cov CycleCovariate" +
" -cov DinucCovariate" +
" -cov TileCovariate" +
" --solid_recal_mode SET_Q_ZERO" +
" -recalFile %s" + parallelism,
1, // just one output file
@ -53,10 +52,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibrator1() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "86b54ba5bc11714787427eb450c0ead8" );
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "0278cce4cfdab869dc0c11d6852a984b" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "344d4252143df8c2cce6b568747553a5");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "2bb3374dde131791d7638031ae3b3e10" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "f6865fee5bbb9e954aad8f9da97277b4" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "064c4a7bdd23974c3a9c5f924540df76" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();