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The battle is over. Picard is revved. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4200 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-09-03 05:28:01 +00:00
parent fdaac4aa78
commit 70bb480939
14 changed files with 25 additions and 25 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
View File

@ -341,7 +341,7 @@ public class IntervalSharder {
nextBin = null;
while(wrappedIterator.hasNext() && nextBin == null) {
Bin bin = wrappedIterator.next();
if(index.getLevelForBin(bin) == index.getNumIndexLevels()-1)
if(index.getLevelForBin(bin) == AbstractBAMFileIndex.getNumIndexLevels()-1)
nextBin = bin;
}
}

2
java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
View File

@ -86,7 +86,7 @@ public class TraverseDuplicates<M,T> extends TraversalEngine<M,T,DuplicateWalker
* @return
*/
protected Set<List<SAMRecord>> uniqueReadSets(List<SAMRecord> reads) {
Set<List<SAMRecord>> readSets = new HashSet<List<SAMRecord>>();
Set<List<SAMRecord>> readSets = new LinkedHashSet<List<SAMRecord>>();
// for each read, find duplicates, and either add the read to its duplicate list or start a new one
for ( SAMRecord read : reads ) {

2
java/test/org/broadinstitute/sting/gatk/walkers/ClipReadsWalkersIntegrationTest.java
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@ -74,7 +74,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
" -OQ -QT 4 -CR WRITE_Q0S" +
" -o %s -ob %s",
2,
Arrays.asList("55c01ccc2e84481b22d3632cdb06c8ba", "12eeaaa8df3d742f68cdd8838b203825"));
Arrays.asList("55c01ccc2e84481b22d3632cdb06c8ba", "22db22749f811d30216215e047461621"));
executeTest("clipOriginalQuals", spec);
}
}

6
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -9,7 +9,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerLod5() {
String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "c4ef635f2597b12b93a73199f07e509b"};
String[] md5s = {"ecff0ce35feb839b6346197db455bbdf", "c4ef635f2597b12b93a73199f07e509b"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
@ -19,7 +19,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerLod50() {
String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "3735a510513b6fa4161d92155e026283"};
String[] md5s = {"ecff0ce35feb839b6346197db455bbdf", "3735a510513b6fa4161d92155e026283"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe",
2,
@ -29,7 +29,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testRealignerKnownsOnly() {
String[] md5s = {"7084d4e543bc756730ab306768028530", "74652bd8240291293ec921f8ecfa1622"};
String[] md5s = {"70b657dcb654bd2c84c38d654c5af697", "74652bd8240291293ec921f8ecfa1622"};
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B:knownIndels,VCF " + validationDataLocation + "NA12878.indels.vcf4 -o %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly",
2,

16
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -52,10 +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", "fd5eca3a40a971d5eabf9ab792bd0295" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "e5d9fc628dcf4f0ae115a6e6cc5423fe");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "7ebdce416b72679e1cf88cc9886a5edc" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "b00679024ce8dcaf611907109a7e9a27" );
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "da79dcc74336a6333f75aeb231590436" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "6c5ac8f71a77f09eec3e38932ba274cf");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "b26a07cc3d3f6a607e786ebcc2c9c8ac" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "504152c1a94d6998af9785bcbddbb3d6" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -106,7 +106,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorMaxQ70() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "0e2bca11d09b1b93bfc4af5c185e0d1d" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "4d24b4683a9b20e93837da75fff2489f" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -163,7 +163,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "a6eb2f8f531164b0a3cb19b4bb1d2f4f" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "85c0500f9f4ba0d613a77d34b5c84a64" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -276,7 +276,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorNoReadGroups() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "474e05b5a0f13776daebeb964a5e0e2b" );
e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "a2d7b780052fe31b0d37fc6462ab58ca" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -331,7 +331,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorNoIndex() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "9733d0c5954dcdf5b9bb0ad0b6eb8232" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "4ae0b3d4e2f6a7c1c60ae64944afff5e" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();

8
java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java
View File

@ -20,8 +20,8 @@ public class DuplicatesWalkersIntegrationTest extends WalkerTest {
List<File> result = executeTest(name, spec).getFirst();
}
@Test public void testChr110Mb() { testCounter("testChr1-10mb", "-L chr1:1-10,000,000 --quietLocus", "fa8bfdd0b62a13a543bae90f7c674db7"); }
@Test public void testIntervalVerbose() { testCounter("testIntervalVerbose", "-L chr1:6,527,154-6,528,292", "1ebcc10b85af16805a54391721776657"); }
@Test public void testChr110Mb() { testCounter("testChr1-10mb", "-L chr1:1-10,000,000 --quietLocus", "d3c329a634904d95c4b180d0d63eadfc"); }
@Test public void testIntervalVerbose() { testCounter("testIntervalVerbose", "-L chr1:6,527,154-6,528,292", "5fbb930020df6ca7d0f724524fc43b3e"); }
public void testCombiner(String name, String args, String md51, String md52) {
WalkerTestSpec spec = new WalkerTestSpec(
@ -35,6 +35,6 @@ public class DuplicatesWalkersIntegrationTest extends WalkerTest {
List<File> result = executeTest(name, spec).getFirst();
}
@Test public void testIntervalCombine() { testCombiner("testIntervalCombine", "-L chr1:6,527,154-6,528,292 -maxQ 50", "d41d8cd98f00b204e9800998ecf8427e", "e2501d7e20564df9f7519fadef8cf283"); }
@Test public void testIntervalCombineQ60() { testCombiner("testIntervalCombine", "-L chr1:6,527,154-6,528,292 -maxQ 60", "d41d8cd98f00b204e9800998ecf8427e", "b23f6436d230f57f969502ddd8d48c18"); }
@Test public void testIntervalCombine() { testCombiner("testIntervalCombine", "-L chr1:6,527,154-6,528,292 -maxQ 50", "d41d8cd98f00b204e9800998ecf8427e", "4541f57820637039bc2f5a97bcaadfe4"); }
@Test public void testIntervalCombineQ60() { testCombiner("testIntervalCombine", "-L chr1:6,527,154-6,528,292 -maxQ 60", "d41d8cd98f00b204e9800998ecf8427e", "8c0350c0a697e4083aab6ead3f404de4"); }
}

BIN
settings/repository/edu.mit.broad/picard-private-parts-1459.jar → settings/repository/edu.mit.broad/picard-private-parts-1562.jar
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2
settings/repository/edu.mit.broad/picard-private-parts-1459.xml → settings/repository/edu.mit.broad/picard-private-parts-1562.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private-parts" revision="1459" status="integration" publication="20100630230000" />
<info organisation="edu.mit.broad" module="picard-private-parts" revision="1562" status="integration" publication="20100902110200" />
</ivy-module>

3
settings/repository/net.sf/picard-1.24.477.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.24.477" status="release" />
</ivy-module>

BIN
settings/repository/net.sf/picard-1.24.477.jar → settings/repository/net.sf/picard-1.29.571.jar
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3
settings/repository/net.sf/picard-1.29.571.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.29.571" status="release" />
</ivy-module>

3
settings/repository/net.sf/sam-1.24.477.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.24.477" status="release" />
</ivy-module>

BIN
settings/repository/net.sf/sam-1.24.477.jar → settings/repository/net.sf/sam-1.29.571.jar
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Binary file not shown.

3
settings/repository/net.sf/sam-1.29.571.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.29.571" status="release" />
</ivy-module>