diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java index bf3ce352a..641bddb2d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java +++ b/public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java @@ -1,6 +1,7 @@ package org.broadinstitute.sting.gatk.filters; import net.sf.picard.filter.SamRecordFilter; +import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; @@ -16,4 +17,18 @@ public abstract class ReadFilter implements SamRecordFilter { * @param engine the engine. */ public void initialize(GenomeAnalysisEngine engine) {} + + + /** + * Determines whether a pair of SAMRecord matches this filter + * + * @param first the first SAMRecord to evaluate + * @param second the second SAMRecord to evaluate + * + * @return true if the SAMRecords matches the filter, otherwise false + * @throws UnsupportedOperationException when paired filter not implemented + */ + public boolean filterOut(final SAMRecord first, final SAMRecord second) { + throw new UnsupportedOperationException("Paired filter not implemented: " + this.getClass()); + } } diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index 0ff6fc244..040845828 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -9,13 +9,13 @@ import java.util.Map; public class IndelRealignerIntegrationTest extends WalkerTest { - private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.bam"; + private static final String mainTestBam = validationDataLocation + "indelRealignerTest.pilot1.ceu.fixed.fixmates.bam"; private static final String mainTestIntervals = validationDataLocation + "indelRealignerTest.pilot1.ceu.intervals"; 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 = "e041186bca9dccf360747c89be8417ad"; - private static final String base_md5_with_SW_or_VCF = "d7c7acd346ee4c8d34f1e2499ff7c313"; + private static final String base_md5 = "7574ab7d0b1ee5d44a0b3f85b6e944e6"; + private static final String base_md5_with_SW_or_VCF = "a918d69d26d3c87b29002ed31f428c48"; @Test public void testDefaults() { @@ -38,7 +38,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec1 = new WalkerTestSpec( baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels, 1, - Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888")); + Arrays.asList("36718f10d523dfb0fa2a709480f24bd4")); executeTest("realigner known indels only from VCF", spec1); } @@ -55,7 +55,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { public void testLods() { HashMap e = new HashMap(); e.put( "-LOD 60", base_md5 ); - e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "f158f18198cf48bbb3d4f1b7127928a3" ); + e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "9a75a0f7ad0442c78d0f8df260e733a4" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -71,7 +71,7 @@ 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("fe39c007d287d372a8137d11c60fbc50")); + Arrays.asList("e98f51d71f0a82141b36a7e9f94db237")); executeTest("realigner long run", spec); } @@ -80,7 +80,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW", 1, - Arrays.asList("e77e59cc6363cf58f392ce5ea8d7e0b6")); + Arrays.asList("58ac675d0699eb236d469b8e84513d11")); executeTest("realigner no output tags", spec); } diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2181.jar b/settings/repository/edu.mit.broad/picard-private-parts-2181.jar deleted file mode 100644 index ef3371827..000000000 Binary files a/settings/repository/edu.mit.broad/picard-private-parts-2181.jar and /dev/null differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2375.jar b/settings/repository/edu.mit.broad/picard-private-parts-2375.jar new file mode 100644 index 000000000..bfa2f65ad Binary files /dev/null and b/settings/repository/edu.mit.broad/picard-private-parts-2375.jar differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2181.xml b/settings/repository/edu.mit.broad/picard-private-parts-2375.xml similarity index 64% rename from settings/repository/edu.mit.broad/picard-private-parts-2181.xml rename to settings/repository/edu.mit.broad/picard-private-parts-2375.xml index d11423b59..b467f934a 100644 --- a/settings/repository/edu.mit.broad/picard-private-parts-2181.xml +++ b/settings/repository/edu.mit.broad/picard-private-parts-2375.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/picard-1.59.1066.xml b/settings/repository/net.sf/picard-1.59.1066.xml deleted file mode 100644 index 73bc3ffee..000000000 --- a/settings/repository/net.sf/picard-1.59.1066.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/picard-1.59.1066.jar b/settings/repository/net.sf/picard-1.67.1197.jar similarity index 62% rename from settings/repository/net.sf/picard-1.59.1066.jar rename to settings/repository/net.sf/picard-1.67.1197.jar index 1bbfd5a19..9243c02df 100644 Binary files a/settings/repository/net.sf/picard-1.59.1066.jar and b/settings/repository/net.sf/picard-1.67.1197.jar differ diff --git a/settings/repository/net.sf/picard-1.67.1197.xml b/settings/repository/net.sf/picard-1.67.1197.xml new file mode 100644 index 000000000..7d9042d6b --- /dev/null +++ b/settings/repository/net.sf/picard-1.67.1197.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/net.sf/sam-1.59.1066.xml b/settings/repository/net.sf/sam-1.59.1066.xml deleted file mode 100644 index 75a327daa..000000000 --- a/settings/repository/net.sf/sam-1.59.1066.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/sam-1.59.1066.jar b/settings/repository/net.sf/sam-1.67.1197.jar similarity index 78% rename from settings/repository/net.sf/sam-1.59.1066.jar rename to settings/repository/net.sf/sam-1.67.1197.jar index 8380da864..8a8343cfa 100644 Binary files a/settings/repository/net.sf/sam-1.59.1066.jar and b/settings/repository/net.sf/sam-1.67.1197.jar differ diff --git a/settings/repository/net.sf/sam-1.67.1197.xml b/settings/repository/net.sf/sam-1.67.1197.xml new file mode 100644 index 000000000..d43aba4ed --- /dev/null +++ b/settings/repository/net.sf/sam-1.67.1197.xml @@ -0,0 +1,3 @@ + + +