Kevin Jacobs

Interesting! I also have a script that computes maximal "wobble" for each variant (prefix or suffix) based on the reference sequence. The major limitation is that the maximum extents in...

@pkrusche: More questions. For some reason I thought `hap.py` and `xcmp` already implemented the consensus intermediate format. Here is the current `xcmp` output from `hap.py` for my first example above...

@david4096: I'm sorry to hear that psam's VCF/BCF support isn't working well. Please let me know if you're having any specific problems and will let you know if they can...

@ljdursi: Accessing INFO and FORMAT values as numpy arrays is a perfectly reasonable feature request. This will push handling of missing values to client code, but that is the trade...

I won't claim to be an expert, but I'll try to find time to review the conversion code.

If you run into any trouble supporting CRAM using pysam, please reach out to Andreas and me. We're happy to rapidly address any problems that you may find. On Fri,...

I agree it would be nice to know a bit more about why CRAM support was failing in conditions other than having to provide an alternative reference file. @AndreasHeger is...

@dcolligan: There is nuance here. AlignmentFile.fetch will return an unmapped reads if another segment is mapped (see section 2, item 4.1 of the SAM specification). If all segments in the...

Please let me know if this appears to be a pysam issue.

Please open a pysam issue. I suspect it is an htslib problem, but I'd like to triage it first and add regression tests to pysam. On Thu, May 12, 2016...