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Temp fix for preSorted=false default.
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src/test/java/htsjdk/beta/codecs/reads/cram/HtsCRAMCodec31Test.java

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -70,7 +70,9 @@ public void testRoundTripCRAM31() throws IOException {
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new ReadsDecoderOptions().setCRAMDecoderOptions(
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new CRAMDecoderOptions().setReferencePath(referencePath));
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final ReadsEncoderOptions readsEncoderOptions =
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new ReadsEncoderOptions().setCRAMEncoderOptions(new CRAMEncoderOptions().setReferencePath(referencePath));
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new ReadsEncoderOptions()
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.setPreSorted(true)
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.setCRAMEncoderOptions(new CRAMEncoderOptions().setReferencePath(referencePath));
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try (final CRAMDecoder cramDecoder = (CRAMDecoder)
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HtsDefaultRegistry.getReadsResolver().getReadsDecoder(sourceCRAMPath, readsDecoderOptions);

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