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Bump htsjdk to 2.23.0
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Diff for: src/com/rtg/simulation/ReadSimEvalCli.java

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@@ -55,6 +55,7 @@
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import htsjdk.samtools.SAMException;
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import htsjdk.samtools.SAMFileHeader;
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import htsjdk.samtools.SAMRecord;
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import htsjdk.samtools.SAMTextHeaderCodec;
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/**
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* Class to calculate
@@ -325,7 +326,7 @@ private void process(final PrintStream out) throws IOException {
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final SamReadingContext context = new SamReadingContext(inputs, 1, filterParams, SamUtils.getUberHeader(inputs), null); // Note, no CRAM support here yet
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try (RecordIterator<SAMRecord> itr = new ThreadedMultifileIterator<>(context, new SingletonPopulatorFactory<>(new SamRecordPopulator()))) {
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if (recordsOut != null) {
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recordsOut.write(itr.header().getTextHeader());
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new SAMTextHeaderCodec().encode(recordsOut, itr.header());
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}
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while (itr.hasNext()) {
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++totalRecords;

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