From cc550b4145bd8f439a46e407ba015eaeea36edea Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Mon, 26 Nov 2012 11:48:05 -0500 Subject: [PATCH 01/12] Add a read and interval on a different contig --- .../traversals/TraverseActiveRegionsTest.java | 27 ++++++++++++++----- 1 file changed, 20 insertions(+), 7 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java index e4c7b2db0..018e92d84 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java @@ -96,8 +96,7 @@ public class TraverseActiveRegionsTest extends BaseTest { intervals.add(genomeLocParser.createGenomeLoc("1", 1000, 1999)); intervals.add(genomeLocParser.createGenomeLoc("1", 2000, 2999)); intervals.add(genomeLocParser.createGenomeLoc("1", 10000, 20000)); - // TODO: this fails! - //intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 20000)); + intervals.add(genomeLocParser.createGenomeLoc("20", 10000, 10100)); intervals = IntervalUtils.sortAndMergeIntervals(genomeLocParser, intervals, IntervalMergingRule.OVERLAPPING_ONLY).toList(); reads = new ArrayList(); @@ -109,8 +108,7 @@ public class TraverseActiveRegionsTest extends BaseTest { reads.add(buildSAMRecord("extended_only", "1", 3000, 3100)); reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990)); reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000)); - // TODO - //reads.add(buildSAMRecord("simple20", "20", 10100, 10150)); + reads.add(buildSAMRecord("simple20", "20", 10025, 10075)); } @Test @@ -204,9 +202,7 @@ public class TraverseActiveRegionsTest extends BaseTest { // extended_only: Extended in 1:2000-2999 // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999 // outside_intervals: none - - // TODO - // simple20: Primary in 20:10000-20000 + // simple20: Primary in 20:10000-10100 Map activeRegions = getActiveRegions(walker, intervals); ActiveRegion region; @@ -221,6 +217,7 @@ public class TraverseActiveRegionsTest extends BaseTest { verifyReadNotPlaced(region, "extended_only"); // TODO: fail verifyReadNonPrimary(region, "extended_and_np"); verifyReadNotPlaced(region, "outside_intervals"); + verifyReadNotPlaced(region, "simple20"); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 1000, 1999)); @@ -232,6 +229,7 @@ public class TraverseActiveRegionsTest extends BaseTest { verifyReadNotPlaced(region, "extended_only"); // TODO: fail verifyReadPrimary(region, "extended_and_np"); verifyReadNotPlaced(region, "outside_intervals"); + verifyReadNotPlaced(region, "simple20"); region = activeRegions.get(genomeLocParser.createGenomeLoc("1", 2000, 2999)); @@ -243,6 +241,19 @@ public class TraverseActiveRegionsTest extends BaseTest { // TODO: fail verifyReadExtended(region, "extended_only"); // TODO: fail verifyReadExtended(region, "extended_and_np"); verifyReadNotPlaced(region, "outside_intervals"); + verifyReadNotPlaced(region, "simple20"); + + region = activeRegions.get(genomeLocParser.createGenomeLoc("20", 10000, 10100)); + + verifyReadNotPlaced(region, "simple"); + verifyReadNotPlaced(region, "overlap_equal"); + verifyReadNotPlaced(region, "overlap_unequal"); + verifyReadNotPlaced(region, "boundary_equal"); + verifyReadNotPlaced(region, "boundary_unequal"); + verifyReadNotPlaced(region, "extended_only"); + verifyReadNotPlaced(region, "extended_and_np"); + verifyReadNotPlaced(region, "outside_intervals"); + verifyReadPrimary(region, "simple20"); // TODO: more tests and edge cases } @@ -282,6 +293,8 @@ public class TraverseActiveRegionsTest extends BaseTest { for (LocusShardDataProvider dataProvider : createDataProviders(intervals)) t.traverse(walker, dataProvider, 0); + t.endTraversal(walker, 0); + return walker.mappedActiveRegions; } From d83ad906eff14027908376eceb37dd502a6fdd78 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Mon, 26 Nov 2012 13:44:13 -0500 Subject: [PATCH 02/12] Add profile range contract --- .../sting/gatk/walkers/ActiveRegionWalker.java | 2 ++ .../traversals/TraverseActiveRegionsTest.java | 17 +++++++++++++++++ 2 files changed, 19 insertions(+) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java index fed2c995e..c6e28df05 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ActiveRegionWalker.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.walkers; +import com.google.java.contract.Ensures; import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broad.tribble.Feature; import org.broadinstitute.sting.commandline.Input; @@ -75,6 +76,7 @@ public abstract class ActiveRegionWalker extends Walker= 0.0", "result.isActiveProb <= 1.0"}) public abstract ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context); // Map over the ActiveRegion diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java index 018e92d84..8a4be48be 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.gatk.traversals; +import com.google.java.contract.PreconditionError; import net.sf.samtools.*; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; @@ -52,6 +53,10 @@ public class TraverseActiveRegionsTest extends BaseTest { this.prob = 1.0; } + public DummyActiveRegionWalker(double constProb) { + this.prob = constProb; + } + @Override public ActivityProfileResult isActive(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { isActiveCalls.add(ref.getLocus()); @@ -132,6 +137,18 @@ public class TraverseActiveRegionsTest extends BaseTest { return activeIntervals; } + @Test (expectedExceptions = PreconditionError.class) + public void testIsActiveRangeLow () { + DummyActiveRegionWalker walker = new DummyActiveRegionWalker(-0.1); + getActiveRegions(walker, intervals).values(); + } + + @Test (expectedExceptions = PreconditionError.class) + public void testIsActiveRangeHigh () { + DummyActiveRegionWalker walker = new DummyActiveRegionWalker(1.1); + getActiveRegions(walker, intervals).values(); + } + @Test public void testActiveRegionCoverage() { DummyActiveRegionWalker walker = new DummyActiveRegionWalker(); From 9bfe39411ee4465860d6cf1a1cb1f0fe32d0a1b3 Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Mon, 26 Nov 2012 14:29:22 -0500 Subject: [PATCH 03/12] Equal overlap should match right/later region --- .../gatk/traversals/TraverseActiveRegionsTest.java | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java index 8a4be48be..66504da11 100644 --- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java @@ -109,7 +109,7 @@ public class TraverseActiveRegionsTest extends BaseTest { reads.add(buildSAMRecord("overlap_equal", "1", 10, 20)); reads.add(buildSAMRecord("overlap_unequal", "1", 10, 21)); reads.add(buildSAMRecord("boundary_equal", "1", 1990, 2009)); - reads.add(buildSAMRecord("boundary_unequal", "1", 1995, 2050)); + reads.add(buildSAMRecord("boundary_unequal", "1", 1990, 2008)); reads.add(buildSAMRecord("extended_only", "1", 3000, 3100)); reads.add(buildSAMRecord("extended_and_np", "1", 990, 1990)); reads.add(buildSAMRecord("outside_intervals", "1", 5000, 6000)); @@ -214,8 +214,8 @@ public class TraverseActiveRegionsTest extends BaseTest { // simple: Primary in 1:1-999 // overlap_equal: Primary in 1:1-999 // overlap_unequal: Primary in 1:1-999 - // boundary_equal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 - // boundary_unequal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 + // boundary_equal: Non-Primary in 1:1000-1999, Primary in 1:2000-2999 + // boundary_unequal: Primary in 1:1000-1999, Non-Primary in 1:2000-2999 // extended_only: Extended in 1:2000-2999 // extended_and_np: Non-Primary in 1:1-999, Primary in 1:1000-1999, Extended in 1:2000-2999 // outside_intervals: none @@ -241,8 +241,8 @@ public class TraverseActiveRegionsTest extends BaseTest { verifyReadNotPlaced(region, "simple"); verifyReadNotPlaced(region, "overlap_equal"); verifyReadNotPlaced(region, "overlap_unequal"); - // TODO: fail verifyReadPrimary(region, "boundary_equal"); - // TODO: fail verifyReadNonPrimary(region, "boundary_unequal"); + // TODO: fail verifyReadNonPrimary(region, "boundary_equal"); + verifyReadPrimary(region, "boundary_unequal"); verifyReadNotPlaced(region, "extended_only"); // TODO: fail verifyReadPrimary(region, "extended_and_np"); verifyReadNotPlaced(region, "outside_intervals"); @@ -253,8 +253,8 @@ public class TraverseActiveRegionsTest extends BaseTest { verifyReadNotPlaced(region, "simple"); verifyReadNotPlaced(region, "overlap_equal"); verifyReadNotPlaced(region, "overlap_unequal"); - // TODO: fail verifyReadNonPrimary(region, "boundary_equal"); - verifyReadPrimary(region, "boundary_unequal"); + verifyReadPrimary(region, "boundary_equal"); + // TODO: fail verifyReadNonPrimary(region, "boundary_unequal"); // TODO: fail verifyReadExtended(region, "extended_only"); // TODO: fail verifyReadExtended(region, "extended_and_np"); verifyReadNotPlaced(region, "outside_intervals"); From 7e4b9c9e6e38a1f20999fa0b6b48a5ce2e313c5f Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 27 Nov 2012 10:12:39 -0500 Subject: [PATCH 05/12] Fix failing unit tests for VariantContextUtilsUnitTest -- Previous version was adding multiple samples with the same name to the variant context --- .../sting/utils/variantcontext/VariantContextUtilsUnitTest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java index f3daa9e4c..3ad438b26 100644 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java @@ -793,7 +793,7 @@ public class VariantContextUtilsUnitTest extends BaseTest { int sampleI = 0; for ( final List alleles : Utils.makePermutations(vc.getAlleles(), 2, true) ) { - genotypes.add(GenotypeBuilder.create("sample" + sampleI, alleles)); + genotypes.add(GenotypeBuilder.create("sample" + sampleI++, alleles)); } genotypes.add(GenotypeBuilder.createMissing("missing", 2)); From 01abcc3e0f718a2ca17e8b182bb642a7926cf2ef Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 27 Nov 2012 14:40:49 -0500 Subject: [PATCH 07/12] Tests didn't like my note to Geraldine in the output logs; apparently it's tested in integration tests --- .../sting/gatk/walkers/diffengine/DiffEngine.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java index 579b84d96..0da23077d 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngine.java @@ -283,7 +283,7 @@ public class DiffEngine { GATKReport report = new GATKReport(); final String tableName = "differences"; // TODO for Geraldine -- link needs to be updated below - report.addTable(tableName, "Summarized differences between the master and test files. See [ask Geraldine to fix link to DiffEngine wiki] for more information", 3); + report.addTable(tableName, "Summarized differences between the master and test files. See http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine for more information", 3); final GATKReportTable table = report.getTable(tableName); table.addColumn("Difference"); table.addColumn("NumberOfOccurrences"); From 79bc878e6a9a280fd7873eca7b2861690dbf2628 Mon Sep 17 00:00:00 2001 From: Menachem Fromer Date: Tue, 27 Nov 2012 22:37:41 -0500 Subject: [PATCH 11/12] Allow debugging to be set from the command line --- .../sting/gatk/walkers/phasing/ReadBackedPhasing.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java index d8ae6b28b..eda43e6a5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java @@ -95,7 +95,8 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr @DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} ) public class ReadBackedPhasing extends RodWalker { - private static final boolean DEBUG = false; + @Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information (if -l DEBUG is also specified)", required = false) + protected boolean DEBUG = false; /** * The VCF file we are phasing variants from. * @@ -949,7 +950,7 @@ public class ReadBackedPhasing extends RodWalker