Pierre Gruet pushed to branch master at Debian Med / htsjdk
Commits: 8cb4ced7 by Pierre Gruet at 2022-12-27T20:21:23+01:00 New upstream version 3.0.4+dfsg - - - - - 7edb8199 by Pierre Gruet at 2022-12-27T20:22:14+01:00 Update upstream source from tag 'upstream/3.0.4+dfsg' Update to upstream version '3.0.4+dfsg' with Debian dir a782c8937dcdc1dc9fb32d3557524067f1216874 - - - - - fc0f99ce by Pierre Gruet at 2022-12-27T20:24:28+01:00 Refreshing patches, one having been upstreamed - - - - - 3ed4136c by Pierre Gruet at 2022-12-27T20:24:52+01:00 Raising Standards version to 4.6.2 (no change) - - - - - d4488418 by Pierre Gruet at 2022-12-27T20:25:13+01:00 Updating changelog - - - - - 2d751565 by Pierre Gruet at 2022-12-27T20:26:08+01:00 Upload to unstable - - - - - 6 changed files: - debian/changelog - debian/control - − debian/patches/130-data-types-in-tests.patch - debian/patches/series - src/main/java/htsjdk/samtools/BAMFileReader.java - src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,11 @@ +htsjdk (3.0.4+dfsg-1) unstable; urgency=medium + + * New upstream version 3.0.4+dfsg + * Refreshing patches + * Raising Standards version to 4.6.2 (no change) + + -- Pierre Gruet <p...@debian.org> Tue, 27 Dec 2022 20:25:59 +0100 + htsjdk (3.0.2+dfsg-1) unstable; urgency=medium * Adding missing DEP-3 headers to patches ===================================== debian/control ===================================== @@ -28,7 +28,7 @@ Build-Depends: default-jdk, libcommons-lang3-java, libjimfs-java, scala-library -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/htsjdk Vcs-Git: https://salsa.debian.org/med-team/htsjdk.git Homepage: https://samtools.github.io/htsjdk/ ===================================== debian/patches/130-data-types-in-tests.patch deleted ===================================== @@ -1,31 +0,0 @@ -Description: in this test, long is expected instead of int -Author: Pierre Gruet <p...@debian.org> -Forwarded: https://github.com/samtools/htsjdk/issues/1631 -Last-Update: 2022-10-31 - ---- a/src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java -+++ b/src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java -@@ -586,18 +586,18 @@ - public Object[][] alignmentStartQueries() { - return new Object[][] { - // cram file, reference, query contig, alignment start query, number of reads with matching alignment start -- {cramQueryWithCRAI, cramQueryReference, "20", 100013, 2}, -- {cramQueryWithLocalCRAI, cramQueryReference, "20", 100013, 2}, -- {cramQueryWithBAI, cramQueryReference, "20", 100013, 2}, -+ {cramQueryWithCRAI, cramQueryReference, "20", 100013L, 2}, -+ {cramQueryWithLocalCRAI, cramQueryReference, "20", 100013L, 2}, -+ {cramQueryWithBAI, cramQueryReference, "20", 100013L, 2}, - // tests to ensure that query results on inputs that have matching reads that are followed by reads - // in the same container that don't match the alignment start are properly constrained to only the - // matching reads - {new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTest.cram"), - new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTest.fa"), -- "Mito", 631, 24}, -+ "Mito", 631L, 24}, - {new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTestGATKGen.cram"), - new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTest.fa"), -- "Mito", 631, 24}, -+ "Mito", 631L, 24}, - }; - } - ===================================== debian/patches/series ===================================== @@ -11,6 +11,5 @@ 110-debian-lib-version.patch disable-network-tests.diff 120-fix-build.patch -130-data-types-in-tests.patch 140-skip-testFlushNotSpammed.patch 150-use-rhino-as-JS-engine.patch ===================================== src/main/java/htsjdk/samtools/BAMFileReader.java ===================================== @@ -175,10 +175,12 @@ public class BAMFileReader extends SamReader.ReaderImplementation { throws IOException { this(useAsynchronousIO ? new AsyncBlockCompressedInputStream(file, inflaterFactory) : new BlockCompressedInputStream(file, inflaterFactory), indexFile!=null ? indexFile : SamFiles.findIndex(file), eagerDecode, useAsynchronousIO, file.getAbsolutePath(), validationStringency, samRecordFactory); - if (mIndexFile != null && mIndexFile.lastModified() < file.lastModified()) { + + if (mIndexFile != null && mIndexFile.lastModified() < file.lastModified() - 5000) { System.err.println("WARNING: BAM index file " + mIndexFile.getAbsolutePath() + " is older than BAM " + file.getAbsolutePath()); } + // Provide better error message when there is an error reading. mStream.setInputFileName(file.getAbsolutePath()); } ===================================== src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java ===================================== @@ -586,18 +586,18 @@ public class HtsCRAMCodec30And21QueryTest extends HtsjdkTest { public Object[][] alignmentStartQueries() { return new Object[][] { // cram file, reference, query contig, alignment start query, number of reads with matching alignment start - {cramQueryWithCRAI, cramQueryReference, "20", 100013, 2}, - {cramQueryWithLocalCRAI, cramQueryReference, "20", 100013, 2}, - {cramQueryWithBAI, cramQueryReference, "20", 100013, 2}, + {cramQueryWithCRAI, cramQueryReference, "20", 100013L, 2}, + {cramQueryWithLocalCRAI, cramQueryReference, "20", 100013L, 2}, + {cramQueryWithBAI, cramQueryReference, "20", 100013L, 2}, // tests to ensure that query results on inputs that have matching reads that are followed by reads // in the same container that don't match the alignment start are properly constrained to only the // matching reads {new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTest.cram"), new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTest.fa"), - "Mito", 631, 24}, + "Mito", 631L, 24}, {new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTestGATKGen.cram"), new HtsPath(TEST_DATA_DIR + "mitoAlignmentStartTest.fa"), - "Mito", 631, 24}, + "Mito", 631L, 24}, }; } View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/c3c6a7c73a8a1fa346070651ff23fe8885aa439b...2d751565d0b18139ccb20b1bb78c12fd4ca4a8ea -- View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/compare/c3c6a7c73a8a1fa346070651ff23fe8885aa439b...2d751565d0b18139ccb20b1bb78c12fd4ca4a8ea You're receiving this email because of your account on salsa.debian.org.
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