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Allow the BAM index to be up to 5 seconds older than the BAM before e… #1634

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Nov 16, 2022
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Allow the BAM index to be up to 5 seconds older than the BAM before e… #1634

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4 changes: 3 additions & 1 deletion src/main/java/htsjdk/samtools/BAMFileReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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());
}
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