Hi All - Release 0.2.0 changes as follows - let me know if you if you have any issue with this one. I'm hoping to get 0.3.0 out by next Sunday with the minimum ORF functionality back in, and will merge this one by then (at latest).
Added
Changelog (history starts here)
Option to redirect all output (reports and SAM) to file prefix and not stdout
Print basic alignment stats upon completion
Show count percentages in UniProt report (both full and basic)
Fixed
Option for minimum ORF length temporarily taken out (to be added in version 0.3.0)
Typo in Uniprot report
A few minor compilation warnings
Changed
Option for minimum ORF length now set to argument "-l". "-o" used for output file prefix
Report type "-u" option starts at 0 now, with 1 being default (full report)
Reorganized usage message to group protein/ORF related options into their own section (to be used more in future development)
Known Issues
Alignment stats shown at completion do not properly subtract out supplementary alignments, so total and percentages are slightly off from flagstat output
File output currently requires prefix to be given, will not autogenerate name if one isn't specified
Hi All - Release 0.2.0 changes as follows - let me know if you if you have any issue with this one. I'm hoping to get 0.3.0 out by next Sunday with the minimum ORF functionality back in, and will merge this one by then (at latest).
Added
Fixed
Changed
Known Issues
@macmanes @tarunaaggarwal @Louisa-Normington @Vadavim @rdbunh @wkthomas