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RNAME and RNEXT fields jumbled on transform BAM->ADAM->BAM #795

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almussel opened this issue Aug 21, 2015 · 4 comments
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RNAME and RNEXT fields jumbled on transform BAM->ADAM->BAM #795

almussel opened this issue Aug 21, 2015 · 4 comments

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@almussel
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About ~10% of reads on the test BAM file I'm using transport the RNAME field to RNEXT on transforming to ADAM and back.

Ex:

ORIGINAL:
PROD103_713:1:1:11748:99410 69 chr20 26271737 0 * = 26271737 0 ...

TRANSFORMED:
PROD103_713:1:1:11748:99410 69 * 0 0 * chr20 26271737 0 ...
@ryan-williams
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Weird! How small of a BAM can you repro this on? Or if you want to point me at the BAM you're using I can try it as well.

@almussel
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Okay, so I discovered that something is funky with the BAM file I'm using (The fields contradict each other). I will see if I can reproduce the issue on a properly formatted BAM.

@heuermh
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heuermh commented Mar 24, 2016

@almussel Can this issue be closed?

@fnothaft
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I believe we did resolve this. Closing.

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4 participants
@heuermh @ryan-williams @fnothaft @almussel