


Usage:

bam_singlemap -d <genome> <bam> | samtools view -Sb - > <new bam>

bam_tally -d <genome> <bam>
bam_gstruct -d <genome> <bam> | iit_store -o <pred>
bam_print -d <genome> -m <genes>,<pred> <bam> <coords>


genecompare -d <genome> -m <genes> <pred.iit> > x, or
genecompare <goldstd.iit> <pred.iit> > x


Depends on samtools and gmap packages.

gfusion depends on gmap and qsub



