Workum, Dirk-Jan van (1aa9ad77) at 22 Mar 23:18
update changelog
Discussion point 3: Which new subcommands should I add to the readthedocs? export_gfa
(which is terribly slow, so only useful for developers ATM) and/or extract_region
?
Workum, Dirk-Jan van (33563295) at 22 Mar 23:13
rename export_pangenome to export_csv and rename convert_pangenome ...
Discussion point 2: Should I add VCF export for extract_region? This is not as trivial as it seems.
Discussion point 1: Should I get the whole pangenome GFA export fast?
Workum, Dirk-Jan van (d67f4466) at 22 Mar 22:57
fix writing of hm PAV data for extract_region
Workum, Dirk-Jan van (933ee1bd) at 22 Mar 20:27
don't crash when no suitable alignment positions are found for alig...
Workum, Dirk-Jan van (51b7f81f) at 20 Mar 23:19
fix gff3 writing for collinearity by reusing other gff3 code
... and 1 more commit
Workum, Dirk-Jan van (d4d63345) at 20 Mar 20:14
small bugfix to simplified gff3 for collinearity ROI
... and 1 more commit
Workum, Dirk-Jan van (dac0c4ef) at 20 Mar 01:04
refactor the use of GenomeRange in GraphRange and add start for col...
... and 4 more commits
Workum, Dirk-Jan van (be1d741f) at 15 Mar 21:53
make alignment method for extract_region multithreaded (over possib...
... and 1 more commit
Workum, Dirk-Jan van (8ce067c9) at 15 Mar 20:29
make GFA output for ROI optional as 1) it's hard to interpret, and ...
Workum, Dirk-Jan van (a6043c47) at 15 Mar 18:57
deal with exception occurring when start position of extract_region...
... and 3 more commits
Workum, Dirk-Jan van (9f49ec4b) at 14 Mar 23:53
adding final TODOs for merge request
Workum, Dirk-Jan van (58051db6) at 14 Mar 22:55
make gene annotations in dbg CSV file unique
... and 1 more commit
Workum, Dirk-Jan van (ae8628f4) at 14 Mar 22:12
adding inner class to store hashsets of arrays by checking content ...
... and 1 more commit