samtools/samtools — pull request #315 by peterjc (2014-11-05 12:57:01+00:00)
Title: FASTQ output from samtools bam2fq even if no qualities.

Alternative fix for bug #313 where samtools bam2fq would produce FASTA records for reads without any quality scores.

Unlike my suggestion on PR #314, as per suggestion on #313 discussion, this instead this always gives FASTQ. When the quality is missing, it uses dummy quality strings of PHRED score 1 (this value could be made into a command line argument).