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rrwick / Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
http://rrwick.github.io/Bandage/
GNU General Public License v3.0
579 stars 96 forks source link

regarding blast hits: fixed a problem displaying them, also allowed more time to compute them #3

Closed rchikhi closed 9 years ago

rchikhi commented 9 years ago

Hi Ryan,

I found a bug when displaying blast hits in "Single" node style. Many hits were not reported, e.g. a reverse-complemented contig which matched full-length to a reference was not reported; turns out the corresponding forward contig had a few small matches.

The cause: hits were filtered such that startPos < endPos, and negative hits were not displayed whenever there existed at least one positive hit.

Also, I'm attaching a commit which raises Blast computation time to 90 seconds instead of 30 seconds, because of a timeout on my machine on larger assemblies. Ideally this could be a tuneable parameter.

rrwick commented 9 years ago

Thank you! It should also be easy to make the BLAST timeout a configurable setting, so I'll go ahead and do that next.

rrwick commented 9 years ago

Okay, I've added a timeout parameter in the BLAST search dialog window. It applies to both building the BLAST database and running the BLAST search.

I'll make a new release in the near future so these fixes are available in the binary builds.

rchikhi commented 9 years ago

Perfect!