[med-svn] [Git][med-team/htsjdk][master] 6 commits: New upstream version 3.0.4+dfsg
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Tue Dec 27 22:25:30 GMT 2022
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 <pgt at 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 <pgt at 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
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