v155-preview2 - 28 Mar. 2007 (not released)
(Pairings)
Code changes:
- Added utility to find SAGE tag locations and take SNP data into account.
(Andy)
- Added support for David's request to underline the cDNA sequence in window,
add a jump link to start of cDNA sequence in window, and open the frameset
there; handle isRC when printing out target coordinates in alignment title.
(Angie)
- Removed customFactoryCheckChromName from customFactory.h. (Angie)
- Added more explicit usage of custom track DB to customFactory.c instead of
relying on hdb routines that call hGetDb, so we can recognize sequence names
as valid for the custom track's DB that may not be hGetDb. Fixed the way that
tdb->type is passed in to the fac->recognizer routines, and the way that they
compare type strings. (Angie)
- Use hGetMinIndexLengthDb instead of kludging around maxChromName in
customFactory.c when loading a custom track that might be for a different DB
from hGetDb. (Angie)
- Updated several makefiles to use common.mk definitions for portability to
cygwin. (Angie)
- Ongoing work on GSID. (Fan, Galt)
- Added/modified logic in several files to support KGIII. (Fan)
- Added PDF/PS top menubar link and supporting output page to hgGenome. (Galt)
- Fixed case issue with new kgIDs in VisiGene. (Galt)
- Added handling routines for cnpSebat2. (Heather)
- More work on HapMap SNPs. (Heather)
- Modified several hgTables files to properly disconnect from custom
track DB. (Hiram)
- Made getCfgValue() a public function from jksql.c, removed from several
files. (Hiram)
- Eliminated duplicate definition of convertEpsToPdf() function in protein
dir, now in src/lib/psGfx.c. (Hiram)
- Ongoing work on KGIII. (Jim)
- Allow missing genome setting in custom track input. (Kate)
- Added support to doRecipBest.pl for scaffold-based target 2, removed use
of DEF file. (Kate)
- More work on Ensembl loading. (Robert)
Data changes:
- Added cnpSebat2 track to hg18. (Heather)
- Added bosTau3 all_est. (Heather)
- Initial work on braFlo1 (lancelet), ce4 genomes. (Hiram)
- More work on oryLat1. (Hiram)
- Finished measurements for equCab1 WindowMasker. (Hiram)
- More work on hg18 multiple alignments. (Kate)