template-length shouldn't use RNAseq reads that span an "N" gap.
revert
added version command
updates to make it a bit easier to track sorting
added a few quick filters - properpairs, noproperpair, etc...
speeling
added nogz option for not compressing temp files - NOTE: THIS METHOD IS SLOW DUE TO PYTHON GZIP IMPL
added command to save FASTQ reads to BAM files (for compression)
Merge branch 'master' into working
Merge branch 'master' into working
added gene filter to tobed output
update for whitelist
revert gtf tobed
update in UTR annotation (make it right)
Merge branch 'working' of ssh://github.com/ngsutils/ngsutils into working
minor output format diff
format issue
introns needed to be sorted first
output junctions for each tid at a time.
need to take into account S operations