v144-final - 9 Oct. 2006

Code changes:

• HTML fixing for hgSession.c and wikiLink.c (Angie)
• Browser build automation scripts moved from src/utils to src/hg/utils/automation (Angie)
• Test for presence of support table for snp125 UI page in hgTrackUi.c and fixes in variation.c and snp.c for SNP tracks including ignoring color sort for older versions of the tracks (Daryl)
• Created omimParseAv.c to parse AV fields of OMIM records, omimCheckAv.c to validate AV positions against protein sequences, and omimParseRec.c to parse OMIM records into files according to field types (Fan)
• Fixed monitor time when JKSQL_TRACE=on (Galt)
• Fixed top bar menu in web.c for cases when user has no cart (Galt)
• Improved error handling and added IUPAC code link for printSnpAlignment2 in hgc.c and added chrom, chromStart and chromEnd to output in snpOrthoJoin.c (Heather)
• Fixes to hgCustom.c, hgGateway.c, and hgTracks.c including passing and maintaining hgsid variable (Hiram)
• Fixes and error handling for customFactory.c (Hiram)
• Added track filter for TFBS track to hgTrackUi.c (Hiram)
• Added sqlMinorVersion() to jksql.c to return minor version of database. Check minor version in dbSnoop.c due to status change with version 4.1 (Hiram)
• Encode spaces on an http GET filename for net.c (Hiram)
• Added help panel and clean up of HTML formatting and bug fixes for hgCustom.c (Kate)
• Fixes in hgTracks.c for browser line visibility and suppression of extra cart variables (Kate)
• Support for displaying genbank misc_difference records (Mark)
• Added function print int table cell in web.c (Mark)
• Added code to handle changes to NCBI CCDS schema (Mark)
• Fixes in gbGetSeqs.c and gbConf.c (Mark)

Data changes:

• Additional pairwise alignments for dp4 and droMoj3 (Angie)
• Added hg18.snp126orthoPanTro2RheMac2 to snp126 rule for all.joiner (Ann)
• Lifted Eddy rnaGene track to hg18 (Robert)
• Added mm8 geneid track (Fan)
• Added chr4 and chr10 to trackDb for encodeRegulomeDnaseArray track on hg17 (Rachel)
• Added BAC end pairs, singles and bad pairs tracks to trackDb and BAC track searches for hgFindSpec for danRer4 (Rachel)
• RepeatMasking finished for bosTau3 (Heather)
• Added TFBS and tfbsConsSites track for hg18 (Hiram)
• Split subtrack groups for encodeNhgriDukeDnaseHs (DNase I track) (Kate)
• hg17 trackDb: experiments with alternate conservation (Kate)
• For hgGene (Known Genes), tables changed that are required to draw the HPRD section (Brooke)