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Uauy-Lab / bioruby-polyploid-tools

Library and tools to deal with polyploid genomics
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--extract_found_contigs option is broken #22

Closed FredericBGA closed 4 years ago

FredericBGA commented 4 years ago

If you try to set --extract_found_contigs option, Polymarker.rb will fail: /polymarker.rb:315:indo_align': undefined local variable or method contigs_f' for main:Object (NameError)

so we maybe need to change: contigs_f to $contigs_f in order to make it a global variable.

or we need to test if --extract_found_contigs is set and then pass the contigs_f as argument to do_align.

I don't know Ruby, so let me know which is the best solution. I can create a PR if you want.

homonecloco commented 4 years ago

I was adding some integration tests, so I took the chance to have a look. Thanks for reporting this, I missed bringing the variable contigs_f when adding support for blast. I didn't try it, as this variable extracts the full chromosome sequence. It is useful when you have fragmented assemblies.