respect gene_id attributes of annotated genes

For which program(s) you want a new feature?
(Capacitor/Simulator/Both/Tetris)
Capacitor

Describe the new feature briefly.
(one sentence summary)
respect gene_id fields

Propose name of command line parameters and/or output attributes.
(e.g., -coolFeature, GTF attribute myCoolFeature=123;)
default output, feature "gene" instead of splicing locus

Feel free to provide any additional information below.
Regarding locus vs. gene_id. I understood from the documentation that
instead of using gene_id from the reference annotation, Flux Capacitor
determines loci independently. However, for our analysis we would very much
like to have read counts per annotated gene as well. Is there a way for
Flux Capacitor to add to locus features an attribute of gene_id that lists
all the gene_ids falling in that locus? And to change the existing gene_id
which lists the chrX:y-z location of the locus to another attribute (for
example location=)?

Original issue reported on code.google.com by gmicha@gmail.com on 12 Aug 2009 at 4:21

sivarajankumar / fluxcapacitor

respect gene_id attributes of annotated genes #17