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v1.7.0

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@timbalam timbalam released this 10 Feb 06:45
· 52 commits to master since this release

BamM v1.7.0 now depends on Samtools 1.0 or greater (recommended Samtools 1.3 at least).

New features (as of v1.6.0) include:

bamm make flag -u or --keep-unmapped will keep unmapped reads in BAM output.
bamm filter flag -v will keep only reads which do not meet specified mapping stringency.

An example application of these features would be using BamM to filter contamined reads, by mapping to a reference using bamm make -u and then running bamm filter -v and extracting the reads (e.g. with samtools fasta).