Pysam pileup limited to 8000 reads

GoogleCodeExporter commented 9 years ago

What steps will reproduce the problem?

import string, sys, pysam, os
inbam = pysam.Samfile( 'lane7.sorted.bam', "rb" )
for pileup_column in inbam.mpileup( reference="chr7", start=140453068, 
end=140453069, stepper="all" ):
    counter = 1
    for read in pileup_column.pileups:
        counter += 1    
    print counter   
inbam.close()

What is the expected output? What do you see instead?
I expect to see more than 8000 reads at a given pileup position.  Pileup seems 
to be capped at 8000 (or so) reads.

What version of the product are you using? On what operating system?
Problem occurs in version 0.3 and 0.4

Please provide any additional information below.

Original issue reported on code.google.com by fcal...@gmail.com on 24 May 2011 at 8:46

GoogleCodeExporter commented 9 years ago

Thanks for bringing this up. 

This limit is set by the samtools library. I have added an explanation to the
pileup() command docstring.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 4 Jun 2011 at 9:10

Changed state: WontFix

GoogleCodeExporter commented 9 years ago

Would mpileup help here, whem you have more than one sample?

Original comment by cas...@gmail.com on 16 Sep 2011 at 4:23

brittneybrinsfield / pysam

Pysam pileup limited to 8000 reads #63