[med-svn] [Git][med-team/htsjdk][upstream] New upstream version 3.0.4+dfsg

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch upstream at Debian Med / htsjdk


Commits:
8cb4ced7 by Pierre Gruet at 2022-12-27T20:21:23+01:00
New upstream version 3.0.4+dfsg
- - - - -


2 changed files:

- src/main/java/htsjdk/samtools/BAMFileReader.java
- src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec30And21QueryTest.java


Changes:

=====================================
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/-/commit/8cb4ced7b5d70cdb80339c6516311d5656151b0d

-- 
View it on GitLab: https://salsa.debian.org/med-team/htsjdk/-/commit/8cb4ced7b5d70cdb80339c6516311d5656151b0d
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