GMOD / GBrowse

the Generic Genome Browser
http://gmod.org/wiki/GBrowse
Other
49 stars 37 forks source link

Fix summary mode for features with no source_tag #55

Closed nathanweeks closed 7 years ago

nathanweeks commented 9 years ago

Summary mode doesn't work for features that lack a source_tag. In the original code below, the $type variable is assumed to contain a string of the form "primary_tag:source_tag", where the source_tag is not a null string; however, in a Bio::DB::SeqFeature::Store::DBI::SQLite database that was loaded loaded from a GFF3 that had "." in the source column, the following types exist:

$ sqlite3 track.db 'select * from typelist;'
1|gene:
2|mRNA:
3|five_prime_UTR:
4|exon:
5|CDS:
6|three_prime_UTR:

This was causing the track to render empty when the user zoomed out to a level that activated summary mode.

The regular expression that sets $basetype was updated to work then the $type variable is of the form "primary_tag:".