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Test file for 'samtools bam2fq'

Tested using samtools post-1.1 develop branch,

Version: 1.1-12-g6f1c154 (using htslib 1.1-14-g912a7d0)

Generated using:

$ ./samtools bam2fq sam_spec_padded.bam > sam_spec_padded.bam2fq.fastq
[M::main_bam2fq] processed 6 reads

Note that SAM conversion is identical:

$ ./samtools bam2fq sam_spec_padded.sam > sam_spec_padded.sam2fq.fastq
[M::main_bam2fq] processed 6 reads
$ diff sam_spec_padded.bam2fq.fastq sam_spec_padded.sam2fq.fastq

Note that conversion of the depadded version is also identical:

$ ./samtools bam2fq sam_spec_padded.depad.bam > sam_spec_padded.depad.bam2fq.fastq
[M::main_bam2fq] processed 6 reads
$ diff sam_spec_padded.bam2fq.fastq sam_spec_padded.depad.bam2fq.fastq
Wrap samtools bam2fq (targetting samtools v1.1)

Tests pass locally with some hackery of paths and binary names.

It seems Galaxy's metadata scripts hit something missing in
samtools v1.1 (they work with samtools v0.1.19), while on the
other hand samtools v1.1 fixes bugs in bam2fq (like knowing to
ignore dummy annotation reads - which my unit test exposes).

This will be problematic to test under TravisCI right now...

Fingers crossed the Galaxy Tool Shed dependency system will allow
this to work nicely with samtools v1.1 for this tool, plus using
the system level samtools v0.1.19 for metadata?