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tseemann / samclip

Filter SAM file for soft and hard clipped alignments
GNU General Public License v3.0
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zero clipping at the beginning of the read #8

Open avilella opened 5 years ago

avilella commented 5 years ago

I googled for a tool like this and I was glad to find it. Thanks @tseemann !

Could an option be added so that --start_max N limits the reads that are accepted if they have more than N clipped bases at the beginning of the read? E.g. for cases like:

4S96M - would be filtered out with --start_max 1 --max 5 96M4S - would not be filtered out with --start_max 1 --max 5

tseemann commented 5 years ago

@avilella am i correct in that you would like separate --max for "start" and "end" ? out of interest, what is the use-case for this behaviour?

avilella commented 5 years ago

Yes, a max for start and one for end.

Thanks in advance

On Mon, 16 Sep 2019, 01:48 Torsten Seemann, notifications@github.com wrote:

@avilella https://github.com/avilella am i correct in that you would like separate --max for "start" and "end" ?

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tseemann commented 5 years ago

@avilella what does "start" mean in a SAM file? I think alignments are always begin..end with begin<end and revcom in a flag?