1.7.3

Change build process to keep built c object in repository so running 'nosetests' actually works.

v1.7.2

User improvements
Warns when creating or parsing a bam file with duplicate reference sequence names, which can cause errors later.
Generates bam index with filtered bam file when using filter mode.

Installation improvements
Simplified autogen script.
Distributed configure script should just work.
Fixed --with-libhts-lib, --with-libhts-inc, --with-libcfu-lib, --with-libcfu-inc flags during setup.

BamM

Fix a segfault in BamM filter mode on some inputs.

v1.7.0

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).