ensure maintenance of BAM file compression

biomedicalinformaticsgroup / Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.

http://biomedicalinformaticsgroup.github.io/Sargasso/

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ensure maintenance of BAM file compression #24

Closed s-heron closed 8 years ago

s-heron commented 8 years ago

Currently when the BAM files are broken down into blocks, this is done through extracting the decompressed data from the 'sambamba view' filestream. This is not space efficient. The filter_reads script can likely be edited to mainatin this compression.

s-heron commented 8 years ago

This is arguably not much of an issue now that the default option is to scrub the block files. What do you reckon Owen?

lweasel commented 8 years ago

Agreed, I'm comfortable with dropping this, if you are.