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Ecogenomics / BamM

Metagenomics-focused BAM file manipulation
http://ecogenomics.github.io/BamM/
GNU Lesser General Public License v3.0
16 stars 7 forks source link

Trimmed mean coverage #3

Closed wwood closed 9 years ago

wwood commented 9 years ago

As well as getting trimmed mean coverage to be included, also changed a few other things so development was simplified (no more messing with pythonpath, and can run this as a dev/testing cmdline). Maybe I was just doing it wrong....

BamM/c$ make && ../bin/bamm parse --coverages /dev/stdout -m tpmean ~/git/BamM/test/data/1_shaddow.bam

Also had issues with incorrect path being specified to the libBamM.a file, but you must have already solved this? Maybe I just broke it (see change in bamm/cWrapper.py)

wwood commented 9 years ago

we also need to homage to the bsd code for pqsort somewhere too I guess, in README/LICENSE. Too tired right now