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simon-anders / htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
https://htseq.readthedocs.io/en/release_0.11.1/
GNU General Public License v3.0
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pysam api supporting #44

Closed lozybean closed 6 years ago

lozybean commented 7 years ago

I would like to compare the cigarstring of two segments, and query_alignment_sequence is very useful to ignore softclip bases. All these properties is in pysam.AlignedSegment API, would you like to keep these property?

iosonofabio commented 7 years ago

Hi, Sorry what part of the htseq API are you referring to? Thanks Fabio

On November 28, 2017 4:47:20 AM PST, Lyon0804 notifications@github.com wrote:

I would like to compare the cigarstring of two segments, and query_alignment_sequence is very useful to ignore softclip bases. All these properties is in pysam.AlignedSegment API, would you like to keep these property?

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lozybean commented 7 years ago

In HTSeq.SAM_Alignment class, I don't know whether it is inherit from pysam.AlignedSegment? but there is some useful property like cigarstring, query_alignment_sequence in pysam.AlignedSegment class, can HTSeq do the same things?

iosonofabio commented 6 years ago

I'm a bit confused, can you provide a minimal example of what you are trying to do? If you can do it with pysam already, what's the matter? HTSeq uses pysam anyway...

lozybean commented 6 years ago

OK, I just try to use HTSeq only. Thank you and sorry for making you confuse.