sam_comp Files

sam_comp(1) and sam_comp2 are alternate versions of the same program,
with priorities set of compressing position sorted data (sam_comp) vs
name sorted data (sam_comp2) with the latter ultimately winning the
SequenceSqueeze contest when ranked by compression ratio.

However in my opiniion this makes sam_comp the better of the two
programs as it fits our usual usage profile, but for historical
reasons sam_comp2 has the higher version number - it came second
basically. Ideally I would amalgamate the two.

For now though sam_comp-0.7 is probably the version you'll most want
to use.

Also note, these are *NOT* generic SAM/BAM compression programs as
they only store the first 11 columns with no support at all for
auxillary fields. They also don't keep the insert size and associated
data. Basically they were designed purely as a fastq compressor,
utilising the fact that when fastq is aligned it can be compressed
higher. As such this is largely an experimental piece of software
created for competition purposes. My long term aim is to get the
technology used here incorporated into existing SAM/BAM compressors
rather than unleash yet another incompatible file format on the
bioinformatics community. We *really* don't need yet more file
formats.

For more generic non-reference based fastq compression see fqzcomp
instead.  For more robust SAM/BAM compression I'd advise checking out
CRAM and/or Goby.