search

ThomasDOtto / ratt

Rapid Annotation Transfer Tool
GNU General Public License v3.0
8 stars 4 forks source link

reconciliation #17

Closed 0xaf1f closed 1 year ago

0xaf1f commented 1 year ago

Incorporated all changes from the Companion version of start.ratt.sh into the current executable ratt. I made no changes of my own other than standardization of whitespace. You can compare using diff -bu to verify that the only remaining differences should be in the interface/CLI argument parsing. Whitespace changes are in a separate commit so as to make review of the parameter changes easier.

My first impression about the Companion version being behind wasn't quite true. It did have the Pacbio parameterSet, but the upstream version had two copies of it (that were slightly different from each other).

Companion did include some changes to nucmer settings for most of the parameterSets, though.

closes #16

haessar commented 1 year ago

Thanks for PR. Could you add the help string from start.ratt.sh (approximate lines 10-60) to the ratt file (adapted for the new way it handles command line options) - then I'm happy to merge.

0xaf1f commented 1 year ago

done