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

After comments from @nh13, updated latest picard and setMateInfo call.

This commit is contained in:
Khalid Shakir 2014-04-08 09:52:04 +08:00
parent cc580ac75f
commit a6b0754990
2 changed files with 13 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
View File

@ -303,7 +303,12 @@ public class ConstrainedMateFixingManager {
}
// we've already seen our mate -- set the mate info and remove it from the map
SamPairUtil.setMateInfo(mate.record, newRead, null);
// Via Nils Homer:
// There will be two SamPairUtil.setMateInfo functions. The default will not update the mate
// cigar tag; in fact, it will remove it if it is present. An alternative SamPairUtil.setMateInfo
// function takes a boolean as an argument ("addMateCigar") and will add/update the mate cigar if
// set to true. This is the one you want to use.
SamPairUtil.setMateInfo(mate.record, newRead, null, true);
if ( reQueueMate ) waitingReads.add(mate.record);
}

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

@ -61,8 +61,8 @@ 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 = "a102dd55451799e5f053c784b762087e";
private static final String base_md5_with_SW_or_VCF = "06b8eefcbd785e929027feaa22bb060d";
private static final String base_md5 = "458588d68c8ea7e54443ea722604b265";
private static final String base_md5_with_SW_or_VCF = "d5ed91bd5b2023c69078a0fc00268d3c";
@Test
public void testDefaults() {
@ -85,7 +85,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
1,
Arrays.asList("1b24b0f2a20aed1adc726d1b296a3192"));
Arrays.asList("a1b9396f4d5b65f7ae6e0062daf363a3"));
executeTest("realigner known indels only from VCF", spec1);
}
@ -102,7 +102,7 @@ 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", "4bf28d3c0337682d439257874377a681" );
e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "dea9bd14323b33348d9cf28e256415f2" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -118,7 +118,7 @@ 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("f4f6c3b2a2be0306a0ecd3def334bafe"));
Arrays.asList("b91c0bf803247f703dc1cb6ccdc4f18f"));
executeTest("realigner long run", spec);
}
@ -127,7 +127,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW",
1,
Arrays.asList("71fb521f8febfe2dc683fc636e28ae7d"));
Arrays.asList("041e2254f271261fb46dc3878cf638f6"));
executeTest("realigner no output tags", spec);
}
@ -149,7 +149,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testMaxReadsInMemory() {
HashMap<String, String> e = new HashMap<String, String>();
e.put("--maxReadsInMemory 10000", base_md5);
e.put("--maxReadsInMemory 10000", "0108cd5950f1a4eb90209c3dca8f9e11");
e.put( "--maxReadsInMemory 40000", base_md5 );
for ( Map.Entry<String, String> entry : e.entrySet() ) {