You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
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.
John Marshall cleaned up some lingering data type problems in the slop tool.
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.
Added a fix for a bug that did not properly handle the splitting of intervals in BED12 records with one block.
Thanks to John Marshall (github: @jmarshall), we have addressed numerical instability issues in the fisher tool.
Thanks to Hao Hou (github: @38), reference genomes can be read as an environment variable (CRAM_REFERENCE) when using CRAM input files.
Added a -rna option to the getfasta tool to allow support for RNA genomes.
Thanks to Hao Hou (github: @38), we fixed input file format detection bugs arising in ZSH.
Thanks to Josh Shapiro (github:@jashapiro) for clarifying a confusing inconsistency in the documentation for the coverage tool.
Thanks to Hao Hou (github: @38), we suppressed unnecessary warnings when reading GZIPP'ed files.
Thanks to Hao Hou (github: @38), we fixed an overflow bug in the shuffle tool.
Thanks to Hao Hou (github: @38), we fixed an data type bug in the shift tool.
Thanks to John Marshall (github: @jmarshall) and Hao Hou (github: @38), we have cleaned up the internal support for htslib.