sync, wip prep_reads

some clarifications in CIGAR operation parsing

fixed find_tag() to use the bam_aux_get()

Daehwan fixed an egregious bug in find_tag()

resync

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

prefiltering seems to work

wip - prefiltering fix

fixed a silly memory release bug

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..

fixed ugly bug in GBamRecord::find_tag()

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

trans.gff3 seems to work

wip gffread trans-splice

gff wip

increased "safe length" for an alignment from 16 to 22

added -a option to control the minimum exact adaptor match to be trimmed at the ends

fqtrim works

fqtrim

adjust safelen threshold from 12 to 16

works

works

fqtrim works

works probably

moved bit handling inlines from GBase to GBitVec

fqtrim

collectSeeds unified

fqtrim reworked

wip fqtrim

wip fqtrim

wip fqtrim

wip fqtrim

wip fqtrim

sync

finally fixed bam_merge

bam_merge needs fixing!

resync

sync back with Daehwan. Test bam_merge for memory leaks!

wip

wip

initial map_report commit

adding map_report (raw counts cuffdiff)

added fq_extract script

wip

added index writing to GBamWriter

adding refactored TinyThread++ code

fix for a subtle XLocus building bug

massive update with Daehwan's work

still working on trans-splicing/fusions in gff

wip

wip: trans-spliced and fusion transcripts

fixed parsing bug for extractAttr(); 
Gstrcmp() and Gstricmp() take a 3rd optional param to make them work like strncmp()

fixed crash when given input file is '-'

added mblasm sources

adding my old mgblast assembler

removed useless operator>

added GBitVec.h; removed operator> requirement for sorted vectors; swap() is now template Gswap()

removed useless operator>

removed useless operator>

spliceCigar() implemented, needs testing

wip spliceCigar() in bwt_map.cpp needs testing

added my mobile fput/fget scripts

wip - SplicedSAMHitFactory() still not implemented

TODO: detect sam/bam input for samopen

GBam working; fixed serious memory leak in GVec::setCapacity()

working

fixed exon positions

wip

wip

minor stats formatting

GBam wip

bamread files

bamread project for testing GBam classes

added GBam BAM reader/writer classes (wip)

fixed calculation of Sn for locus

fix locus Sn calculation

gbs2gff fixes

Ensembl conversion corrections

fixed horrendous bug in GList.hh (resizing GVec)

backup scripts updated

gb2gff tweaks

added backup scripts, improved conversion for NCBI human annotation

wip

minor script updates

added GStr::reverse(), GAlnExtend stringency tweaks

made more stringent on the 5' end, other tests and fixes

wip GYarn (threads)

wip - works?

fixed GVec, GArray to use new[] instead of malloc

wip

wip

adjusting params

adjusting params

wip

wip

by default bam2fastx shows unmapped only

moved match_LeftEnd() and match_RightEnd() to GAlnExtend

wip

added gapped alignment extension code

switching to gclib/GAlnExtend

extended 'x' code to also include interleaved exons on opposite strand

reverseChars() minor edit

separate wrappers for 5' and  3' alignments

starting to add polyA/T trimming

disable pointer arithmetic in GXGreedyExtend(), it's bad

fixed a few more subtle bugs

rewrote, set params X=8, M=2, N=3

wip bad

wip

wip

fixes, still a bug with flast_d[d] = flast_d[d] - flower + 2;

wip

wip, fixed memory leaks

3' match seems to work, needs a few refinements

wip - cutting seeds, finalize()

u

implementing GreedyAlign for best rseeds etc.

added seqalign files

creating seqalign storage

reversed gene_id requirement for TSS clustering

gridx fixed to export PERL5LIB and PYTHONPATH

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

made some Flybase GFF3 "errors" non-fatal

made sure the order of XLoci is maintained during clustering

added --force-exons option to force "exon" subfeatures

removed startChanged flag, not needed

made sure Swap (Exchange) is available for GList, GVec

finally fixed the placeGf clustering bug

fixed buglet in fix_umrnas() comparing strand to 0 instead of '.'

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