wip

RPS20P29, ENSG00000241828 not collapsing

RPS20P29, ENSG00000241828 not collapsing

debug RPS20P29 ENSG00000241828 not collapsing

reclass_XStrand fixed for 's' not code being reported if 'i' was found

fix direct CDS segment given as the only subfeature

fixed a loading bug when a CDS was given to a monoFeature() with a self-exon

minor edits

longest CDS is now kept on -MK containment

when collapsing redundant transcripts, transfer CDS coords to the container if it doesn't have any

fixed GStr[-2] bug

added gfview files

added gfview

m

minor edit

added fix for fileExists() under MSVC

added clview files and examples

clview added

wip

wip

wip segment_juncs

wip conversion to SAM processing

adding bam2fastx as recognized unpacker for .bam files

trying to get rid of unspliced_bwt in Maps (replace by unspliced_sam)

added SeqAn to tophat source pack

adding tophat source work

adding tophat_cpp dir

added missing gff_utils source

adding misc scripts

various scripts

added recent fix for no TSS-cluster if different GeneID

added cuffcompare sources

mkdir cuffcompare

added a few more source files, test code

sync with local source

sync with local source

sync with local src

added old trimpoly code just for archive

sync with my local source

added qv-threshold trimming

update l5,l3 to defaults if no trimming is performed

bugfix: prevent crash with -o option is not given

fixed bug causing overtrimming

added cdbfasta source files

mkdir cdbfasta

added gffread sources

mkdir gffread

initial commit

mkdir

added my gclib source files

import