File Changes for cline

v258_preview to v258_preview2 (2011-09-27 to 2011-10-04) v258

• src/hg/inc/hdb.h
  • lines changed 13, context: html, text, full: html, text
    Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
• src/hg/lib/hdb.c
  • lines changed 38, context: html, text, full: html, text
    Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
• src/hg/makeDb/doc/proteins/101005.txt
  • lines changed 2, context: html, text, full: html, text
    Updated the documentation in the build script to indicate the tables used only by the proteome browser (thanks, Fan)
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 34, context: html, text, full: html, text
    Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
• src/hg/makeDb/schema/all.joiner
  • lines changed 6, context: html, text, full: html, text
    Added a relationship between the tRNAName field in kgXref and the name field in the tRNAs table
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 1, context: html, text, full: html, text
    Fixed an HTML error that left much of the methods section represented as a hyperlink
  • lines changed 39, context: html, text, full: html, text
    Put back the old content of knownGene.html. Moved the new content to knownGeneNew.html
• src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
  • lines changed 156, context: html, text, full: html, text
    Put back the old content of knownGene.html. Moved the new content to knownGeneNew.html
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 50, context: html, text, full: html, text
    Setting out to support two versions of the UCSC Genes details page: the old one on beta and RR, and a new one on alpha only. Trying to achieve this with two new trackDb.ra stanzas for knownGene (one for beta and RR, one for alpha), which should override the stanza in trackDb/trackDb.ra for hg19 only
  • lines changed 1, context: html, text, full: html, text
    Just learned that when you use the html qualifier, you shouldn't list your html filename with the html suffix
• src/hg/rnaStructure/utrFa/utrFa.c
  • lines changed 13, context: html, text, full: html, text
    Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines