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sam_comp-0.9.tar.gz 2014-08-19 46.3 kB 22 weekly downloads
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README 2012-08-14 1.4 kB 11 weekly downloads
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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.
Source: README, updated 2012-08-14