Commits for angie

v248_preview2 to v248_base (2011-03-01 to 2011-03-08) v248

• Feature #2820 ((tabix: add as optional linked library in kent/src):one last makefile target that wasn't using ${L}, caught by 'make test'.
  • src/hg/autoSql/tests/makefile - lines changed 1, context: html, text, full: html, text
• Track #1656 (GWAS Catalog): monthly data update on hgwdev.
  • src/hg/makeDb/doc/hg18.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 3, context: html, text, full: html, text
• Bug #2917 (DGV colors need changing): oops, I let the new descriptionsneak out to the RR before the track! Adding the old description back for beta,public versions. It should be removed again when we push v10.
  • src/hg/makeDb/trackDb/human/dgvOldColors.html - lines changed 77, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
• Track #1684 (SNPs 132 (dbSNP)): Brooke noticed that all PAR SNPs werecounted as multiply-mapped -- I added an exception to snpNcbiToUcsc's logic that detects multiply-mapped SNPs to take a bed4 file specifying PAR regions, and allow a SNP to map once to the same PAR on both X and Y without counting it as multiply mapped. Still need to update doDbSnp.pl to dump $db.par if it exists and apply the new option to snpNcbiToUcsc.
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 114, context: html, text, full: html, text
• Enabling next/prev-exon arrows for DECIPHER track at b0b's request.Those arrows are implemented for linkedFeatures, so I convert the bed4 DECIPHER items into linkedFeatures during loading, and use lf->extra to store the phenotypes string used in draw and mapItems.
  • src/hg/hgTracks/simpleTracks.c - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
• hgTrackDb now supports an SSI-like syntax for track .html files toinsert the contents of other files, so multiple tracks' html files can share text: <!-- #insert file="relativePathToSharedText.html" --> And the snp132* tracks (#1684) now use this: the shared description text is in snp132.shared.html, and the four track .htmls all use the new syntax to insert the shared text.
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp132.html - lines changed 355, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp132.shared.html - lines changed 355, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp132Common.html - lines changed 351, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp132NonUnique.html - lines changed 351, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/snp132Patient.html - lines changed 351, context: html, text, full: html, text
• Added description of hgTrackDb's new support for #insert'ing a file'scontents (git show b9b57796) into track .html files to trackDb/README.
  • src/hg/makeDb/trackDb/README - lines changed 14, context: html, text, full: html, text