1. Thanks to Hao Hou (github: @38), we have made substantial improvements in the speed associated with parsing input files and in printing results. It turns our that these tasks consume a large proportion of run time, especially as input files increase in size. These changes result in a 2-3X improvement in speed, depending on input types, options, etc.
2. Thanks to John Marshall (github: @jmarshall), who improved the stability and cleanliness of the code used for random number generation. These changes also squash a bug that arises on Debian systems.
3. John Marshall cleaned up some lingering data type problems in the slop tool.
4. Thanks to @gringer for adding the -ignoreD option to the genomecov tool, which allows D CIGAR operations to be ignored when calculating coverage. This is useful for long-read technologies with high INDEL error rates.
5. Added a fix for a bug that did not properly handle the splitting of intervals in BED12 records with one block.
6. Thanks to John Marshall (github: @jmarshall), we have addressed numerical instability issues in the fisher tool.
7. Thanks to Hao Hou (github: @38), reference genomes can be read as an environment variable (CRAM_REFERENCE) when using CRAM input files.
8. Added a -rna option to the getfasta tool to allow support for RNA genomes.
9. Thanks to Hao Hou (github: @38), we fixed input file format detection bugs arising in ZSH.
10. Thanks to Josh Shapiro (github:@jashapiro) for clarifying a confusing inconsistency in the documentation for the coverage tool.
11. Thanks to Hao Hou (github: @38), we suppressed unnecessary warnings when reading GZIPP'ed files.
12. Thanks to Hao Hou (github: @38), we fixed an overflow bug in the shuffle tool.
13. Thanks to Hao Hou (github: @38), we fixed an data type bug in the shift tool.
14. Thanks to John Marshall (github: @jmarshall) and Hao Hou (github: @38), we have cleaned up the internal support for htslib.