zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

The underlying bam file for this test was busted for many reasons preventing Picard folks from making unrelated changes, so I needed to fix it. Updating md5s accordingly. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5943 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-06-03 22:26:06 +00:00
parent ac3f1be7f0
commit b93829e505
1 changed files with 7 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -10,12 +10,12 @@ import java.util.Map;
public class IndelRealignerIntegrationTest extends WalkerTest { public class IndelRealignerIntegrationTest extends WalkerTest {
private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.bam"; private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.bam";
private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals"; private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals";
private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf"; 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 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 baseCommand = baseCommandPrefix + "-o %s ";
private static final String base_md5 = "28c045a821e541820a049595759fe962"; private static final String base_md5 = "d7c7acd346ee4c8d34f1e2499ff7c313";
@Test @Test
public void testDefaults() { public void testDefaults() {
@ -45,13 +45,13 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec1 = new WalkerTestSpec( WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "-knownsOnly -B:indels,vcf " + knownIndels, baseCommand + "-knownsOnly -B:indels,vcf " + knownIndels,
1, 1,
Arrays.asList("ea91283e0af5432c1d63b052ed3dcfe4")); Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888"));
executeTest("realigner known indels only from VCF", spec1); executeTest("realigner known indels only from VCF", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec( WalkerTestSpec spec2 = new WalkerTestSpec(
baseCommand + "-knownsOnly -D " + GATKDataLocation + "dbsnp_129_b36.rod", baseCommand + "-knownsOnly -D " + GATKDataLocation + "dbsnp_129_b36.rod",
1, 1,
Arrays.asList("3eed07873a474d8d8d4935399c99f793")); Arrays.asList("78850024ac9ff3ba51b6f097c7041c1d"));
executeTest("realigner known indels only from dbsnp", spec2); executeTest("realigner known indels only from dbsnp", spec2);
} }
@ -59,7 +59,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
public void testLods() { public void testLods() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( "-LOD 60", base_md5 ); e.put( "-LOD 60", base_md5 );
e.put( "-LOD 1", "9a59cd8508f72f8935410b6fb2e6e7d3" ); e.put( "-LOD 1", "f158f18198cf48bbb3d4f1b7127928a3" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -84,7 +84,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseCommand + "--noOriginalAlignmentTags", baseCommand + "--noOriginalAlignmentTags",
1, 1,
Arrays.asList("4bbd9a0d998bc0483cd9bbbdac8cb9c2")); Arrays.asList("e77e59cc6363cf58f392ce5ea8d7e0b6"));
executeTest("realigner no output tags", spec); executeTest("realigner no output tags", spec);
} }
@ -106,7 +106,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test @Test
public void testMaxReadsInMemory() { public void testMaxReadsInMemory() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( "--maxReadsInMemory 10000", "87605e2dea24d3e01efaeec5f44e8671" ); e.put( "--maxReadsInMemory 10000", "d7c7acd346ee4c8d34f1e2499ff7c313" );
e.put( "--maxReadsInMemory 40000", base_md5 ); e.put( "--maxReadsInMemory 40000", base_md5 );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {