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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almussel commented Aug 21, 2015

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 ...

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ryan-williams Aug 21, 2015

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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.

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ryan-williams commented Aug 21, 2015

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.

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almussel Aug 21, 2015

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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.

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almussel commented Aug 21, 2015

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.

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heuermh Mar 24, 2016

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@almussel Can this issue be closed?

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heuermh commented Mar 24, 2016

@almussel Can this issue be closed?

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fnothaft Mar 24, 2016

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I believe we did resolve this. Closing.

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fnothaft commented Mar 24, 2016

I believe we did resolve this. Closing.

@fnothaft fnothaft closed this Mar 24, 2016

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