pileup on streaming SAM records

[winni2k]

I have a use case where I want to implement a read-group-aware samtools mpileup on a file streamed from stdin or a UNIX file descriptor. I think this could be done with pysam's pileup engine, but my testing shows that pileup requires an indexed BAM. Is there an easy way to get the pileup to work on SAM/BAM records streamed from stdin? If we assume that the reads are position sorted, then this should be feasible, no?

[jmarshall]

The samtools mpileup command works fine when reading SAM from stdin, so certainly the underlying HTSlib pileup engine works with such input.

What pysam code have you considered, and did it result in a “pileup of samfiles not implemented yet” exception?

[winni2k]

Here is what I ran. test2.bam has no index. I am not asking for a particular region in pileup, so an index should not be necessary. Likewise, if I am pileing up from stdin, then an index won't be available either.

Is there another way to do this?

In [1]: import pysam

In [2]: f = pysam.AlignmentFile('test2.bam', 'rb')

In [3]: for r in f.pileup():
   ...:     r
   ...:
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-3-387591687760> in <module>
----> 1 for r in f.pileup():
      2     r
      3

pysam/libcalignmentfile.pyx in pysam.libcalignmentfile.AlignmentFile.pileup()

ValueError: no index available for pileup

This is running pysam 0.15.3

[jmarshall]

Try applying PR #916 and rebuilding pysam.

[winni2k]

Nice! I'll have a go.