From b64bb144b353dfe4f4aa784bdade1293210e9e70 Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Thu, 17 Jan 2019 14:24:12 -0500 Subject: [PATCH] Update htsjdk to 2.18.2 (#5585) * Updating htsjdk 2.18.1 -> 2.18.2 * Remove deprecated method use * Changing IntervalUtilsUnitTest due to changes in IntervalList * IntervalList now rejects certain invalid intervals that it previously didn't and throw IllegalArgumentException. * This ends up changing which exceptions are thrown in some cases, updated some tests to accept both MalformedFile and MalforedGenomeLoc. --- build.gradle | 2 +- .../datasources/VariantsSparkSinkUnitTest.java | 15 +++++++++------ .../hellbender/utils/IntervalUtilsUnitTest.java | 4 ++-- 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/build.gradle b/build.gradle index 57004bb0bb9..98accf09a42 100644 --- a/build.gradle +++ b/build.gradle @@ -58,7 +58,7 @@ repositories { } final requiredJavaVersion = "8" -final htsjdkVersion = System.getProperty('htsjdk.version','2.18.1') +final htsjdkVersion = System.getProperty('htsjdk.version','2.18.2') final picardVersion = System.getProperty('picard.version','2.18.16') final barclayVersion = System.getProperty('barclay.version','2.1.0') final sparkVersion = System.getProperty('spark.version', '2.2.0') diff --git a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java index 96521a11108..f2de9fe5eae 100644 --- a/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/engine/spark/datasources/VariantsSparkSinkUnitTest.java @@ -3,16 +3,19 @@ import com.google.common.io.Files; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; -import htsjdk.samtools.SamStreams; import htsjdk.samtools.seekablestream.SeekablePathStream; import htsjdk.samtools.seekablestream.SeekableStream; import htsjdk.samtools.util.BlockCompressedInputStream; +import htsjdk.samtools.util.IOUtil; import htsjdk.variant.utils.VCFHeaderReader; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.GenotypeBuilder; import htsjdk.variant.variantcontext.VariantContext; import htsjdk.variant.variantcontext.VariantContextBuilder; -import htsjdk.variant.vcf.*; +import htsjdk.variant.vcf.VCFConstants; +import htsjdk.variant.vcf.VCFHeader; +import htsjdk.variant.vcf.VCFHeaderLine; +import htsjdk.variant.vcf.VCFStandardHeaderLines; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; @@ -20,15 +23,15 @@ import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.broadinstitute.hellbender.CommandLineProgramTest; +import org.broadinstitute.hellbender.GATKBaseTest; import org.broadinstitute.hellbender.engine.spark.SparkContextFactory; import org.broadinstitute.hellbender.exceptions.UserException; +import org.broadinstitute.hellbender.testutils.MiniClusterUtils; +import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.broadinstitute.hellbender.tools.IndexFeatureFile; import org.broadinstitute.hellbender.utils.Utils; import org.broadinstitute.hellbender.utils.gcs.BucketUtils; import org.broadinstitute.hellbender.utils.io.IOUtils; -import org.broadinstitute.hellbender.GATKBaseTest; -import org.broadinstitute.hellbender.testutils.MiniClusterUtils; -import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; @@ -236,7 +239,7 @@ private void checkFileExtensionConsistentWithContents(String outputPath) throws private static String getVcfFormat(String outputFile) throws IOException { try (InputStream in = openFile(outputFile)) { BufferedInputStream bis = new BufferedInputStream(in); // so mark/reset is supported - return inferFromUncompressedData(SamStreams.isGzippedSAMFile(bis) ? new GZIPInputStream(bis) : bis); + return inferFromUncompressedData(IOUtil.isGZIPInputStream(bis) ? new GZIPInputStream(bis) : bis); } } diff --git a/src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java index 1f1ac0c1d42..499f4e820a3 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java @@ -1134,7 +1134,7 @@ public void testInvalidGATKFileIntervalHandling(GenomeLocParser genomeLocParser, IntervalUtils.loadIntervals(intervalArgs, IntervalSetRule.UNION, IntervalMergingRule.ALL, 0, genomeLocParser); } - @Test(expectedExceptions=UserException.MalformedFile.class, dataProvider="invalidIntervalTestData") + @Test(expectedExceptions={UserException.MalformedFile.class, UserException.MalformedGenomeLoc.class}, dataProvider="invalidIntervalTestData") public void testLoadIntervalsInvalidPicardIntervalHandling(GenomeLocParser genomeLocParser, String contig, int intervalStart, int intervalEnd ) throws Exception { @@ -1177,7 +1177,7 @@ public void testIntervalFileToListNegativeOneLength(GenomeLocParser genomeLocPar IntervalUtils.intervalFileToList(genomeLocParser, picardIntervalFile.getAbsolutePath()); } - @Test(expectedExceptions=UserException.CouldNotReadInputFile.class, dataProvider="invalidIntervalTestData") + @Test(expectedExceptions={UserException.CouldNotReadInputFile.class, UserException.MalformedGenomeLoc.class}, dataProvider="invalidIntervalTestData") public void testIntervalFileToListInvalidPicardIntervalHandling(GenomeLocParser genomeLocParser, String contig, int intervalStart, int intervalEnd ) throws Exception {