fixed ugly bug in GBamRecord::find_tag()

trans.gff3 seems to work

wip gffread trans-splice

gff wip

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

fqtrim works

adjust safelen threshold from 12 to 16

works

fqtrim works

moved bit handling inlines from GBase to GBitVec

fqtrim

fqtrim reworked

wip fqtrim

wip fqtrim

wip fqtrim

adding refactored TinyThread++ code

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()

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

TODO: detect sam/bam input for samopen

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

fixed exon positions

wip

GBam wip

added GBam BAM reader/writer classes (wip)

fixed horrendous bug in GList.hh (resizing GVec)

added GStr::reverse(), GAlnExtend stringency tweaks

wip GYarn (threads)

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

adjusting params

wip

moved match_LeftEnd() and match_RightEnd() to GAlnExtend

added gapped alignment extension code

reverseChars() minor edit

made some Flybase GFF3 "errors" non-fatal

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

RPS20P29, ENSG00000241828 not collapsing

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

added fix for fileExists() under MSVC

added a few more source files, test code

sync with local source

added my gclib source files

import