------------------- - Adjust logging to not crash if username/hostname not available
0.6
------------------- - Extended to support pysam v0.13, v0.14 - Added optional command line arg to specify length of unique molecular tag (UMT) - Added optional command line arg to sort filters results by name instead of count - Added validation to check for properly paired alignments - Added validation to check for presence of secondary alignments - Adjusted so warning instead of error when no families found - Substantial refactors to clarify implementation
0.5.1
---------------- - Extended supported python and pysam versions - Adjusted to avoid performance problem when processing extremely deep pileups - Adjusted so that when no families pass filters show warning instead of error message (thanks to ccario83 for upvoting this fix)
0.5
--------------- - Filters now exclude supplemental alignments - Added BAM tags to show pair positions and CIGAR values - Reduced required memory and improved performance
0.4
--------------- - Added input/command validations - Added annotated bam option - Revised QUICKSTART, METHODS - Added PG line in BAM header - Improved logging of filtered aligns and progress - Removed some logged stats to focus logging results - Removed dependency on pandas/numpy - Moderate performance (speed) improvements in calculating consensus sequence - Switched consensus quality to be the max mapping quality
0.3
--------------- - Added filters to exclude low quality, unmapped, or unpaired alignments - Revised BAM tags; documented BAM tags in BAM header - Extended logging to write to file and console - Adjusted to make deterministic in Py3/Py2