resuming works

wip - tophat adding resume features (need to add setRunStage())

wip tophat.py - adding resume feature

updated to v2.0.4

update

sync with Daehwan's fixes

fix_map_ordering wip to throw away not "acceptable" mappings

fixed the prefilter bug, I think

wip, -M option still broken!

merge-sync attempt

seems to work, before sync

wip prep_reads

wip!!!

wip tophat

wip tophat accepted_hits

wip prep_reads.cpp, tophat

wip

wip

sync, wip prep_reads

resync

prefilter works, but it eliminates too many reads (!)

prefiltering seems to work

wip - prefiltering fix

working, writing rejected.bam

almost working with bam all over

prep_reads now writes bam

bam read support complete, now to make prep_reads conversion..

misaligned extra bowtie command fixed

wip -- still errors in logs!

wip: prep_reads from/to BAM

removed symlink

wip 

updated

silly bug fix

more fixes for bam2fastx.cpp

fixed bam2fastx bugs

added -P option to write paired reads, and compression

sync

finally fixed bam_merge

bam_merge needs fixing!

resync

sync back with Daehwan. Test bam_merge for memory leaks!

wip

wip

wip

added index writing to GBamWriter

massive update with Daehwan's work

spliceCigar() implemented, needs testing

wip spliceCigar() in bwt_map.cpp needs testing

wip - SplicedSAMHitFactory() still not implemented

wip

by default bam2fastx shows unmapped only

wip : spliceCigar()

wip - implementing SplicedSAMHitFactory::get_hit_from_buf()

first attempt at accepting different Color qvlen in prep_reads

fixed segment_juncs to work with .bam files

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