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@@ -244,15 +244,16 @@ else if (rec1.getReadUnmappedFlag() && rec2.getReadUnmappedFlag()) { |
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mapped.setMateAlignmentStart(unmapped.getAlignmentStart());
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mapped.setMateNegativeStrandFlag(unmapped.getReadNegativeStrandFlag());
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mapped.setMateUnmappedFlag(true);
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- // For the mapped read, set it's mateCigar to null, since the other read must be unmapped
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+ mapped.setAttribute(SAMTag.MQ.name(), null);
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mapped.setAttribute(SAMTag.MC.name(), null);
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mapped.setInferredInsertSize(0);
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unmapped.setMateReferenceIndex(mapped.getReferenceIndex());
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unmapped.setMateAlignmentStart(mapped.getAlignmentStart());
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unmapped.setMateNegativeStrandFlag(mapped.getReadNegativeStrandFlag());
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unmapped.setMateUnmappedFlag(false);
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- // For the unmapped read, set it's mateCigar to the mate's Cigar, since the mate must be mapped
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+ unmapped.setAttribute(SAMTag.MQ.name(), mapped.getMappingQuality());
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+ // For the unmapped read, set mateCigar to the mate's Cigar, since the mate must be mapped
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if (setMateCigar) unmapped.setAttribute(SAMTag.MC.name(), mapped.getCigarString());
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else unmapped.setAttribute(SAMTag.MC.name(), null);
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unmapped.setInferredInsertSize(0);
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