Update: adaptation of a default run bam->pileup on my small test dataset gives 
the same result in my case using mpileup instead of pileup in the sam_pileup.py 
script (line 97).
Not tested any additional parameters though so there might be subtle 
differences in the outcome.


    #prepare basic pileup command
    cmd = 'samtools mpileup %s -f %s %s > %s'
    try:



Van: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: vrijdag 20 juli 2012 12:20
Aan: 'galaxy-dev@lists.bx.psu.edu'
Onderwerp: [galaxy-dev] samtools pileup deprecated

Hi All,

Maybe I missed it on the list here, but it seems that for samtools the pileup 
command has been deprecated without backward compatibility from the more recent 
samtools packages...
http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html

Did anyone rewrite some of the samtools tool wrappers for this....?
I am currently testing whether the Bam->pileup command can be easily changed in 
the sam_pileup.py script. But some functionality has gone and some additional 
is there. It seems I am up-to-date with the latest wrappers in the galaxy_dist 
repository.

Any pointers to recent wrappers would be welcomed.

Alex



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