Hello all,

Further to recent discussions about dealing with large
FASTQ files, and the short term advantages of gzipped
FASTQ as a filetype in Galaxy (or gzipped files in general,
https://bitbucket.org/galaxy/galaxy-central/issue/666/ ), we
also discussed the merits of unaligned BAM files.

It occurred to me this could be defined in Galaxy as
subclass of the existing BAM definition, with a simple
sniffer based on running "samtools idxstats" to find out
if there are any mapped reads or not.

This would then make it easy for tools capable of
aligning SAM/BAM to list unaligned-bam as a Galaxy
input format (avoiding complications of realigning
previously aligned reads).

You could also have a matching aligned BAM
subclass, then tools like SNP detectors should
insist on an aligned BAM file for input.

Does this sound reasonable?

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