On Tue, Nov 4, 2014 at 2:44 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
Hi all,
I'm looking for a little advice on the pre-existing SAM/BAM filtering tools already in the Galaxy Tool Shed (to avoid reinventing the wheel).
As I mentioned on another thread, I'm working on a wrapper for the "samtools bam2fq" command (targeting samtools 1.1 which fixed some bugs in this tool and added new functionality compared to samtools 0.1.19), see:
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_bam2fq https://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq
Going off topic, but I just hit a problem here: https://github.com/samtools/samtools/issues/313
Depending on if the reads have a QUAL value or not, samtool bam2fq will produce either FASTA or FASTQ output - and will happily give a mixture in one file. I know Heng Li has a parser that will take this kind of input, but Galaxy likes to have well defined file formats.
I may have to "fix" samtools, perhaps by adding a strict FASTQ output mode?
Peter