samtools/samtools — pull request #314 by peterjc (2014-11-05 12:02:40+00:00)
Title: samtools bam2qf option to force FASTA or FASTQ output

This addresses issue #313 - the current behaviour (left as the default) produces a mixture of FASTQ and FASTA depending on if each individual read has quality scores or not.

While some tools/parsers will handle mixed files like this, others will have trouble. This is a problem with systems like Galaxy with a strict datatype system.

I wanted to use ``-O`` for the new output format argument (to follow the pattern set in ``samtools sort``/``rmdup``/``fixmate``) but that is already taken for the original quality option, thus ``-F`` instead.

Note that if ``samtools bam2fq`` is called forcing FASTQ output, this currently will use a default PHRED quality score one 1. This value might make sense to add as a further command line option? (I will add this on request, suggestions for the command line argument name welcome)