From 64d990b29be90fbc333d974a3f94314d3ef4f7df Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Tue, 4 Sep 2018 17:46:30 -0400 Subject: [PATCH] upgrading to htsjdk 2.16.1 --- build.gradle | 2 +- .../org/broadinstitute/hellbender/tools/GatherVcfsCloud.java | 2 +- .../org/broadinstitute/hellbender/utils/GenotypeUtils.java | 4 ++-- .../org/broadinstitute/hellbender/utils/spark/SparkUtils.java | 2 +- 4 files changed, 5 insertions(+), 5 deletions(-) diff --git a/build.gradle b/build.gradle index ce1d4776173..1d1d7ebf356 100644 --- a/build.gradle +++ b/build.gradle @@ -57,7 +57,7 @@ repositories { } final requiredJavaVersion = "8" -final htsjdkVersion = System.getProperty('htsjdk.version','2.16.0') +final htsjdkVersion = System.getProperty('htsjdk.version','2.16.1') final picardVersion = System.getProperty('picard.version','2.18.7') final barclayVersion = System.getProperty('barclay.version','2.1.0') final sparkVersion = System.getProperty('spark.version', '2.2.0') diff --git a/src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java b/src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java index dc78f4df4e8..7c199f7ad84 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/GatherVcfsCloud.java @@ -411,7 +411,7 @@ private static void gatherWithBlockCopying(final List vcfs, final File out // If we found the end of the header then write the remainder of this block out as a // new gzip block and then break out of the while loop if (firstNonHeaderByteIndex >= 0) { - final BlockCompressedOutputStream blockOut = new BlockCompressedOutputStream(out, null); + final BlockCompressedOutputStream blockOut = new BlockCompressedOutputStream(out, (Path)null); blockOut.write(blockContents, firstNonHeaderByteIndex, blockContents.length - firstNonHeaderByteIndex); blockOut.flush(); // Don't close blockOut because closing underlying stream would break everything diff --git a/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java index 58786e1e915..61d603cf671 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/GenotypeUtils.java @@ -62,14 +62,14 @@ public static GenotypeCounts computeDiploidGenotypeCounts(final VariantContext v final Allele a1 = g.getAllele(0); final Allele a2 = g.getAllele(1); if (a2.isNonReference()) { - final int[] idxVector = vc.getGLIndecesOfAlternateAllele(a2); + final int[] idxVector = vc.getGLIndicesOfAlternateAllele(a2); idxAA = idxVector[0]; idxAB = idxVector[1]; idxBB = idxVector[2]; } //I expect hets to be reference first, but there are no guarantees (e.g. phasing) else if (a1.isNonReference()) { - final int[] idxVector = vc.getGLIndecesOfAlternateAllele(a1); + final int[] idxVector = vc.getGLIndicesOfAlternateAllele(a1); idxAA = idxVector[0]; idxAB = idxVector[1]; idxBB = idxVector[2]; diff --git a/src/main/java/org/broadinstitute/hellbender/utils/spark/SparkUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/spark/SparkUtils.java index 586f4904d2f..37c1d2448da 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/spark/SparkUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/spark/SparkUtils.java @@ -80,7 +80,7 @@ public static void convertHeaderlessHadoopBamShardToBam( final File bamShard, fi * @param outputStream stream to write the SAM header to */ private static void writeBAMHeaderToStream( final SAMFileHeader samFileHeader, final OutputStream outputStream ) { - final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null); + final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, (File)null); final BinaryCodec outputBinaryCodec = new BinaryCodec(new DataOutputStream(blockCompressedOutputStream)); final String headerString;