On Tue, Nov 4, 2014 at 2:44 PM, Peter Cock <p.j.a.c...@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:

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?

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