Fixed bug where SamPairUtil.setMateInfo() would omit the MQ tag if on… #647
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@ktibbett Want to take a quick look at this? This will effect |
| @@ -246,12 +246,14 @@ else if (rec1.getReadUnmappedFlag() && rec2.getReadUnmappedFlag()) { | |||
| mapped.setMateUnmappedFlag(true); | |||
| // For the mapped read, set it's mateCigar to null, since the other read must be unmapped | |||
| mapped.setAttribute(SAMTag.MC.name(), null); | |||
| mapped.setAttribute(SAMTag.MQ.name(), null); | |||
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move to before setting the MC since that's the order elsewhere: it makes it easier to find.
| mapped.setInferredInsertSize(0); | ||
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| unmapped.setMateReferenceIndex(mapped.getReferenceIndex()); | ||
| unmapped.setMateAlignmentStart(mapped.getAlignmentStart()); | ||
| unmapped.setMateNegativeStrandFlag(mapped.getReadNegativeStrandFlag()); | ||
| unmapped.setMateUnmappedFlag(false); | ||
| unmapped.setAttribute(SAMTag.MQ.name(), mapped.getMappingQuality()); | ||
| // For the unmapped read, set it's mateCigar to the mate's Cigar, since the mate must be mapped |
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I know it was like that before...can you remove the ' from "it's"
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👍 though I protest that this class lacks tests...we should at least open a ticket to record this fact... |
…e read was mapped and the other unmapped.
tfenne
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Updates applied. @yfarjoun If we logged issues for everything that needed testing... we'd have a lot of issues 😞 . |
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👍 |
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Description
Fix a small but annoying bug that was causing unmapped reads with mapped mates to get most mate information set except
MQwhich is set in all other cases.Checklist
…e read was mapped and the other unmapped.