The --refContigs option is shared by cactus-pangenome and cactus-graphmap-split. But during a recent refactor, it apparently stopped working in the latter, which is under a bit lest testing. No matter what you gave to cactus-graphmap-split --refContigs, it would assume the option was empty and determine its own reference contigs. The same option in cactus-pangenome worked fine, however.
Anyway, this PR should fix this issue. And is probably worth a patch release once it passes its tests.
The
--refContigsoption is shared bycactus-pangenomeandcactus-graphmap-split. But during a recent refactor, it apparently stopped working in the latter, which is under a bit lest testing. No matter what you gave tocactus-graphmap-split --refContigs, it would assume the option was empty and determine its own reference contigs. The same option incactus-pangenomeworked fine, however.Anyway, this PR should fix this issue. And is probably worth a patch release once it passes its tests.
Resolves #1078