Output NH tag in SAM output

COMBINE-lab / RapMap

Rapid sensitive and accurate read mapping via quasi-mapping

GNU General Public License v3.0

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Output NH tag in SAM output #8

Closed vals closed 8 years ago

vals commented 8 years ago

I just tried the 'quasialignment' (SA based) and it is positively amazing! (~15 seconds per sample to map)

Would it be possible to output an NH tag in the SAM output which tells how many locations a read maps to?

rob-p commented 8 years ago

Hi @vals --- I'm glad you may find a use for RapMap. We're also somewhat amazed by the speed with which it seems possible to attack this problem. It should be fairly easy to add this tag to the current output. I'm assigning this issue to myself and will comment here when I've implemented this feature.

rob-p commented 8 years ago

Ok, I've added the NH flag to the output alignments, so I'm going to close this issue for now. However, feel free to comment / re-open if necessary.