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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

BamM build process changes #36

Closed timbalam closed 8 years ago

timbalam commented 8 years ago

The idea is that the setup.py script won't need to run the autoconf process. Towards this, configure scripts, and Makefile.in for the packaged dependencies generated by the autoconf process are included in the git repository.

The autoconf process can be done if needed using a new autogen.sh script which calls autoreconf in a way that seems to work properly.

Works on my machine.

wwood commented 8 years ago

I had a brief look, seems good. If you are happy a new release is warranted I think.

timbalam commented 8 years ago

Additionally, the new release will check for duplicate bam reference sequence names after the make step and before the parse step, as this is not allowed in bam files and can lead to crashes and possibly incorrect results. Also, the filter step will automatically generate an index file for the filtered bam file.