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- Fixed problems in BAM output:
- Corrected next reference in paired reads
- Excludes reads where CIGAR is entirely clipped
- Unpairs reads which had no mate in input
- Added BAM tags to excluded reads (useful when --preserving_all_reads)
- Adjusted to improve performance (about 6x faster)
- Added support for pip install
- Added functional tests
- Added support for travis CI
- Added support for Python3
- Added support for pysam 0.8.3