On Thu, Apr 19, 2012 at 1:55 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi Brad & Lance,
> I've been using Brad's bam_to_bigwig tool in Galaxy but realized
> today (with a new dataset using a splice-aware mapper) that it
> doesn't seem to be ignoring CIGAR N operators where a read is
> split over an intron. Looking over Brad's Python script which
> calculates the coverage to write an intermediate wiggle file, this is
> done with the samtools via pysam. It is not obvious to me if this
> can be easily modified to ignore introns. Is this possible Brad?

Looking into this a bit more, perhaps 'samtools depth' might
be useful (bam2depth.c), maybe we can use this code to update
your python+pysam code?

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