breseq v0.36.0
·
130 commits
to master
since this release
- Fixed an issue causing JC evidence to not save info in annotated GD files.
- Fixed a crash when annotating GD files containing INV mutations.
- Fixed empty line at the end of the FASTQ input causing an error.
- Major updates to gdtools commands.
- gdtools COMPARE/ANNOTATE
- New TABLE format that provides a text (CSV) version of HTML style compare table.
- TEXT_* output columns added if -b option provided.
- Changed HTML default to not repeat header lines for easier loading into Excel.
If you liked these, you can add them back as before with --repeat-header 10.
- gdtools FILTER/REMOVE
- Added the ability to preserve evidence entries.
- Added control over commenting/removing filtered lines, renumbering IDs, and verbose messages.
- Fixed (and explained) logic for matching the UNDEFINED value
- New ASSIGNED field for filtering on whether evidence is used.
- Added some examples of usage to the command line help.