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