diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index 275ababda..185082c2d 100644 --- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -60,8 +60,8 @@ 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() { @@ -84,7 +84,7 @@ 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); } @@ -101,7 +101,7 @@ 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", "4bf28d3c0337682d439257874377a681" ); + e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "dea9bd14323b33348d9cf28e256415f2" ); for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( @@ -117,7 +117,7 @@ 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); } @@ -126,7 +126,7 @@ 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); } @@ -148,7 +148,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { @Test public void testMaxReadsInMemory() { HashMap e = new HashMap(); - e.put( "--maxReadsInMemory 10000", base_md5 ); + e.put( "--maxReadsInMemory 10000", "0108cd5950f1a4eb90209c3dca8f9e11" ); e.put( "--maxReadsInMemory 40000", base_md5 ); for ( Map.Entry entry : e.entrySet() ) { diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java index b421a2bd7..ebb387a8c 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java @@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.io.storage; import net.sf.samtools.*; import net.sf.samtools.util.CloseableIterator; +import net.sf.samtools.util.ProgressLoggerInterface; import net.sf.samtools.util.RuntimeIOException; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub; @@ -149,4 +150,8 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage, StingSAMFileWrite public void close() { outputTracker.getStorage(this).close(); } + + /** + * @throws java.lang.UnsupportedOperationException No progress logging in this implementation. + */ + @Override + public void setProgressLogger(final ProgressLoggerInterface logger) { + throw new UnsupportedOperationException("Progress logging not supported"); + } } diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java index 9ad388adf..e4210f280 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java @@ -205,7 +205,7 @@ public class VariantContextWriterStub implements Stub, Var if ( doNotWriteGenotypes ) options.add(Options.DO_NOT_WRITE_GENOTYPES); if ( engine.lenientVCFProcessing() ) options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER); - if ( indexOnTheFly && ! isCompressed() ) options.add(Options.INDEX_ON_THE_FLY); + if ( indexOnTheFly) options.add(Options.INDEX_ON_THE_FLY); if ( forceBCF || (getOutputFile() != null && VariantContextWriterFactory.isBCFOutput(getOutputFile())) ) options.add(Options.FORCE_BCF); diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java index fbbaa6636..caf45142f 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java @@ -29,10 +29,11 @@ import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import org.broad.tribble.index.Index; +import org.broad.tribble.index.MutableIndex; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.utils.SequenceDictionaryUtils; -import java.util.LinkedHashSet; +import java.util.List; import java.util.Map; import java.util.Set; import java.util.TreeSet; @@ -70,23 +71,29 @@ public class IndexDictionaryUtils { * @param dict the sequence dictionary to add contigs to * @return the filled-in sequence dictionary */ - static SAMSequenceDictionary createSequenceDictionaryFromContigList(Index index, SAMSequenceDictionary dict) { - LinkedHashSet seqNames = index.getSequenceNames(); + static SAMSequenceDictionary createSequenceDictionaryFromContigList(final Index index, final SAMSequenceDictionary dict) { + final List seqNames = index.getSequenceNames(); if (seqNames == null) { return dict; } - for (String name : seqNames) { + for (final String name : seqNames) { SAMSequenceRecord seq = new SAMSequenceRecord(name, 0); dict.addSequence(seq); } return dict; } + /** + * Sets the sequence dictionary of the given index. THE INDEX MUST BE MUTABLE (i.e. not Tabix). + * + * @param index the (mutable) index file to use + * @param dict the dictionary to use + */ public static void setIndexSequenceDictionary(Index index, SAMSequenceDictionary dict) { for ( SAMSequenceRecord seq : dict.getSequences() ) { final String contig = IndexDictionaryUtils.SequenceDictionaryPropertyPredicate + seq.getSequenceName(); final String length = String.valueOf(seq.getSequenceLength()); - index.addProperty(contig,length); + ((MutableIndex)index).addProperty(contig, length); } } diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java index 5c74bb5b8..8755cedac 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java @@ -26,8 +26,8 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.SAMFileHeader; -import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMRecord; +import net.sf.samtools.util.ProgressLoggerInterface; import org.broadinstitute.sting.gatk.io.StingSAMFileWriter; import java.util.ArrayList; @@ -119,4 +119,12 @@ public class ArtificialStingSAMFileWriter implements StingSAMFileWriter { @Override public void setMaxRecordsInRam(int maxRecordsInRam) { } + + /** + * @throws java.lang.UnsupportedOperationException No progress logging in this implementation. + */ + @Override + public void setProgressLogger(final ProgressLoggerInterface logger) { + throw new UnsupportedOperationException("Progress logging not supported"); + } } diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java index 4cd361ba1..728ec5597 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java @@ -26,6 +26,7 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.*; +import net.sf.samtools.util.ProgressLoggerInterface; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID; import org.broadinstitute.sting.utils.Utils; @@ -174,4 +175,11 @@ public class NWaySAMFileWriter implements SAMFileWriter { public void close() { for ( SAMFileWriter w : writerMap.values() ) w.close(); } + + @Override + public void setProgressLogger(final ProgressLoggerInterface logger) { + for (final SAMFileWriter writer: writerMap.values()) { + writer.setProgressLogger(logger); + } + } } diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java index 4ad17aef5..1a471383a 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java @@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMRecord; +import net.sf.samtools.util.ProgressLoggerInterface; /** * XXX @@ -77,4 +78,9 @@ public class SimplifyingSAMFileWriter implements SAMFileWriter { read.setAttribute("RG", rg); return read; } + + @Override + public void setProgressLogger(final ProgressLoggerInterface logger) { + dest.setProgressLogger(logger); + } } diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java index 5a160566e..8f0b385b4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java @@ -194,14 +194,13 @@ public class GATKVCFUtils { public static IndexCreator getIndexCreator(GATKVCFIndexType type, int parameter, File outFile) { IndexCreator idxCreator; switch (type) { - case DYNAMIC_SEEK: idxCreator = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); break; - case DYNAMIC_SIZE: idxCreator = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SIZE); break; - case LINEAR: idxCreator = new LinearIndexCreator(); break; - case INTERVAL: idxCreator = new IntervalIndexCreator(); break; + case DYNAMIC_SEEK: idxCreator = new DynamicIndexCreator(outFile, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); break; + case DYNAMIC_SIZE: idxCreator = new DynamicIndexCreator(outFile, IndexFactory.IndexBalanceApproach.FOR_SIZE); break; + case LINEAR: idxCreator = new LinearIndexCreator(outFile, parameter); break; + case INTERVAL: idxCreator = new IntervalIndexCreator(outFile, parameter); break; default: throw new IllegalArgumentException("Unknown IndexCreator type: " + type); } - idxCreator.initialize(outFile, parameter); return idxCreator; } diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java index 57020424c..e5b49dc65 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java +++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java @@ -43,6 +43,7 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.File; +import java.lang.reflect.Method; import java.util.Arrays; import java.util.Collections; import java.util.Set; @@ -94,36 +95,44 @@ public class GATKVCFUtilsUnitTest extends BaseTest { private final GATKVCFIndexType type; private final int parameter; private final Class expectedClass; - private final int expectedDefaultBinSize; - private final int expectedBinSize; + private final Integer expectedDimension; + private final Method dimensionGetter; - private IndexCreatorTest(GATKVCFIndexType type, int parameter, Class expectedClass, int expectedDefaultBinSize, int expectedBinSize) { + private IndexCreatorTest(GATKVCFIndexType type, int parameter, Class expectedClass, Integer expectedDimension, + String dimensionGetterName) { super(IndexCreatorTest.class); this.type = type; this.parameter = parameter; this.expectedClass = expectedClass; - this.expectedDefaultBinSize = expectedDefaultBinSize; - this.expectedBinSize = expectedBinSize; + this.expectedDimension = expectedDimension; + try { + // Conditional matches testGetIndexCreator's if-statement + this.dimensionGetter = this.expectedDimension == null ? null : expectedClass.getDeclaredMethod(dimensionGetterName); + } catch (NoSuchMethodException e) { + throw new RuntimeException(e); + } } } @DataProvider(name = "indexCreator") public Object[][] indexCreatorData() { - new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SEEK, 0, DynamicIndexCreator.class, -1, -1); - new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SIZE, 0, DynamicIndexCreator.class, -1, -1); - new IndexCreatorTest(GATKVCFIndexType.LINEAR, 100, LinearIndexCreator.class, LinearIndexCreator.DEFAULT_BIN_WIDTH, 100); - new IndexCreatorTest(GATKVCFIndexType.INTERVAL, 200, IntervalIndexCreator.class, IntervalIndexCreator.DEFAULT_FEATURE_COUNT, 200); + new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SEEK, 0, DynamicIndexCreator.class, null, null); + new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SIZE, 0, DynamicIndexCreator.class, null, null); + new IndexCreatorTest(GATKVCFIndexType.LINEAR, 100, LinearIndexCreator.class, 100, "getBinSize"); + new IndexCreatorTest(GATKVCFIndexType.INTERVAL, 200, IntervalIndexCreator.class, 200, "getFeaturesPerInterval"); return IndexCreatorTest.getTests(IndexCreatorTest.class); } @Test(dataProvider = "indexCreator") - public void testGetIndexCreator(IndexCreatorTest spec) { + public void testGetIndexCreator(IndexCreatorTest spec) throws Exception{ File dummy = new File(""); IndexCreator ic = GATKVCFUtils.getIndexCreator(spec.type, spec.parameter, dummy); Assert.assertEquals(ic.getClass(), spec.expectedClass, "Wrong IndexCreator type"); - Assert.assertEquals(ic.defaultBinSize(), spec.expectedDefaultBinSize, "Wrong default bin size"); - Assert.assertEquals(ic.getBinSize(), spec.expectedBinSize, "Wrong bin size"); + if (spec.expectedDimension != null) { + Integer dimension = (int)spec.dimensionGetter.invoke(ic); + Assert.assertEquals(dimension, spec.expectedDimension, "Wrong dimension"); + } } } \ No newline at end of file diff --git a/public/repo/net/sf/picard/1.107.1683/picard-1.107.1683.jar b/public/repo/net/sf/picard/1.109.1722/picard-1.109.1722.jar similarity index 89% rename from public/repo/net/sf/picard/1.107.1683/picard-1.107.1683.jar rename to public/repo/net/sf/picard/1.109.1722/picard-1.109.1722.jar index 089b71385..38d1e5958 100644 Binary files a/public/repo/net/sf/picard/1.107.1683/picard-1.107.1683.jar and b/public/repo/net/sf/picard/1.109.1722/picard-1.109.1722.jar differ diff --git a/public/repo/net/sf/picard/1.107.1683/picard-1.107.1683.pom b/public/repo/net/sf/picard/1.109.1722/picard-1.109.1722.pom similarity index 90% rename from public/repo/net/sf/picard/1.107.1683/picard-1.107.1683.pom rename to public/repo/net/sf/picard/1.109.1722/picard-1.109.1722.pom index fd8a61917..075b2606e 100644 --- a/public/repo/net/sf/picard/1.107.1683/picard-1.107.1683.pom +++ b/public/repo/net/sf/picard/1.109.1722/picard-1.109.1722.pom @@ -3,23 +3,23 @@ 4.0.0 net.sf picard - 1.107.1683 + 1.109.1722 picard net.sf sam - 1.107.1683 + 1.109.1722 org.broadinstitute variant - 1.107.1683 + 1.109.1722 org.broad tribble - 1.107.1683 + 1.109.1722 diff --git a/public/repo/net/sf/sam/1.107.1683/sam-1.107.1683.jar b/public/repo/net/sf/sam/1.109.1722/sam-1.109.1722.jar similarity index 71% rename from public/repo/net/sf/sam/1.107.1683/sam-1.107.1683.jar rename to public/repo/net/sf/sam/1.109.1722/sam-1.109.1722.jar index 928838707..88a396a9e 100644 Binary files a/public/repo/net/sf/sam/1.107.1683/sam-1.107.1683.jar and b/public/repo/net/sf/sam/1.109.1722/sam-1.109.1722.jar differ diff --git a/public/repo/net/sf/sam/1.107.1683/sam-1.107.1683.pom b/public/repo/net/sf/sam/1.109.1722/sam-1.109.1722.pom similarity index 95% rename from public/repo/net/sf/sam/1.107.1683/sam-1.107.1683.pom rename to public/repo/net/sf/sam/1.109.1722/sam-1.109.1722.pom index 89114f546..59a0e5df7 100644 --- a/public/repo/net/sf/sam/1.107.1683/sam-1.107.1683.pom +++ b/public/repo/net/sf/sam/1.109.1722/sam-1.109.1722.pom @@ -3,7 +3,7 @@ 4.0.0 net.sf sam - 1.107.1683 + 1.109.1722 sam-jdk diff --git a/public/repo/org/broad/tribble/1.107.1683/tribble-1.107.1683.jar b/public/repo/org/broad/tribble/1.109.1722/tribble-1.109.1722.jar similarity index 67% rename from public/repo/org/broad/tribble/1.107.1683/tribble-1.107.1683.jar rename to public/repo/org/broad/tribble/1.109.1722/tribble-1.109.1722.jar index efa04ad2c..7b60393ee 100644 Binary files a/public/repo/org/broad/tribble/1.107.1683/tribble-1.107.1683.jar and b/public/repo/org/broad/tribble/1.109.1722/tribble-1.109.1722.jar differ diff --git a/public/repo/org/broad/tribble/1.107.1683/tribble-1.107.1683.pom b/public/repo/org/broad/tribble/1.109.1722/tribble-1.109.1722.pom similarity index 87% rename from public/repo/org/broad/tribble/1.107.1683/tribble-1.107.1683.pom rename to public/repo/org/broad/tribble/1.109.1722/tribble-1.109.1722.pom index 7bf169bd4..21ab0d712 100644 --- a/public/repo/org/broad/tribble/1.107.1683/tribble-1.107.1683.pom +++ b/public/repo/org/broad/tribble/1.109.1722/tribble-1.109.1722.pom @@ -3,13 +3,13 @@ 4.0.0 org.broad tribble - 1.107.1683 + 1.109.1722 tribble net.sf sam - 1.107.1683 + 1.109.1722 diff --git a/public/repo/org/broadinstitute/variant/1.107.1683/variant-1.107.1683.jar b/public/repo/org/broadinstitute/variant/1.109.1722/variant-1.109.1722.jar similarity index 94% rename from public/repo/org/broadinstitute/variant/1.107.1683/variant-1.107.1683.jar rename to public/repo/org/broadinstitute/variant/1.109.1722/variant-1.109.1722.jar index ea4ebe35e..273b32d60 100644 Binary files a/public/repo/org/broadinstitute/variant/1.107.1683/variant-1.107.1683.jar and b/public/repo/org/broadinstitute/variant/1.109.1722/variant-1.109.1722.jar differ diff --git a/public/repo/org/broadinstitute/variant/1.107.1683/variant-1.107.1683.pom b/public/repo/org/broadinstitute/variant/1.109.1722/variant-1.109.1722.pom similarity index 90% rename from public/repo/org/broadinstitute/variant/1.107.1683/variant-1.107.1683.pom rename to public/repo/org/broadinstitute/variant/1.109.1722/variant-1.109.1722.pom index 256963812..5e393b752 100644 --- a/public/repo/org/broadinstitute/variant/1.107.1683/variant-1.107.1683.pom +++ b/public/repo/org/broadinstitute/variant/1.109.1722/variant-1.109.1722.pom @@ -3,18 +3,18 @@ 4.0.0 org.broadinstitute variant - 1.107.1683 + 1.109.1722 variant org.broad tribble - 1.107.1683 + 1.109.1722 net.sf sam - 1.107.1683 + 1.109.1722 org.apache.commons diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml index 00788c94b..6e7a51217 100644 --- a/public/sting-root/pom.xml +++ b/public/sting-root/pom.xml @@ -43,7 +43,7 @@ -Xmx${test.maxmemory} -XX:+UseParallelOldGC -XX:ParallelGCThreads=${java.gc.threads} -XX:GCTimeLimit=${java.gc.timeLimit} -XX:GCHeapFreeLimit=${java.gc.heapFreeLimit} - 1.107.1683 + 1.109.1722 ${picard.public.version} ${picard.public.version} ${picard.public.version}