File Changes for tdreszer

v283_preview to v283_preview2 (2013-04-23 to 2013-04-30) v283

• src/hg/htdocs/style/HGStyle.css
  • lines changed 22, context: html, text, full: html, text
    Added styles for gene haplotype alleles section of hgGene which will soon be checked in.
  • lines changed 3, context: html, text, full: html, text
    In moving haplotypes to be cart persistent, toggling visibility by class helps.
  • lines changed 2, context: html, text, full: html, text
    Collapsed 2 button styles into 1 for haplotypes.
• src/hg/inc/cart.h
  • lines changed 5, context: html, text, full: html, text
    Added cartTimeoutBoolean, which allows setting a var to true and having it timeout after a given number of hours.
• src/hg/inc/genePred.h
  • lines changed 15, context: html, text, full: html, text
    Added routines for getting genePred coding DNA and determining coding position. To be used in haplotypes code about to be checked in.
• src/hg/inc/haplotypes.h
  • lines changed 274, context: html, text, full: html, text
    First check-in of the bluk of code for geneAlleles tool and hgGene's 'Gene Haplotype Alleles' section. This haplotype code, still evolving, relies upon vcf files (1000 Genomes phase 1) to discover sets of individual variants within a protein coding gene model that are segregating as distinct haplotypes. Ongoing work is expected to strengthen scoring routines for better highlighting of unexpected results. Haplotypes are currently only built for protein coding genes, but can certainly be expanded to cover other gene models and indeed, an region of the genome.
  • lines changed 10, context: html, text, full: html, text
    Reworked the haplotypes section of hgGene for persistence of cart vars (they will timeout after 3 days) and added reset to default. Given that the section is scrolled out of visible range and that some display options can be burdensome, it seemed fitting that cart vars will expire when not actively used.
• src/hg/js/alleles.js
  • lines changed 352, context: html, text, full: html, text
    Adding alleles.js which will handle the Gene Haploptype Alleles section of hgGene. Since this section could be added to hgc for any genePred model, the js code is not being put into a 'hgGene' specific file.
  • lines changed 67, context: html, text, full: html, text
    Reworked the haplotypes section of hgGene for persistence of cart vars (they will timeout after 3 days) and added reset to default. Given that the section is scrolled out of visible range and that some display options can be burdensome, it seemed fitting that cart vars will expire when not actively used.
  • lines changed 34, context: html, text, full: html, text
    More experimentation on buttons/controls with Brooke for haplotypes. At this point, we agree to leave things as they are until a wider audience has a chance to weigh in.
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding alleles.js which will handle the Gene Haploptype Alleles section of hgGene. Since this section could be added to hgc for any genePred model, the js code is not being put into a 'hgGene' specific file.
• src/hg/js/utils.js
  • lines changed 14, context: html, text, full: html, text
    Adding alleles.js which will handle the Gene Haploptype Alleles section of hgGene. Since this section could be added to hgc for any genePred model, the js code is not being put into a 'hgGene' specific file.
• src/hg/lib/cart.c
  • lines changed 31, context: html, text, full: html, text
    Added cartTimeoutBoolean, which allows setting a var to true and having it timeout after a given number of hours.
• src/hg/lib/genePred.c
  • lines changed 92, context: html, text, full: html, text
    Added routines for getting genePred coding DNA and determining coding position. To be used in haplotypes code about to be checked in.
• src/hg/lib/haplotypes.c
  • lines changed 3340, context: html, text, full: html, text
    First check-in of the bluk of code for geneAlleles tool and hgGene's 'Gene Haplotype Alleles' section. This haplotype code, still evolving, relies upon vcf files (1000 Genomes phase 1) to discover sets of individual variants within a protein coding gene model that are segregating as distinct haplotypes. Ongoing work is expected to strengthen scoring routines for better highlighting of unexpected results. Haplotypes are currently only built for protein coding genes, but can certainly be expanded to cover other gene models and indeed, an region of the genome.
  • lines changed 206, context: html, text, full: html, text
    Reworked the haplotypes section of hgGene for persistence of cart vars (they will timeout after 3 days) and added reset to default. Given that the section is scrolled out of visible range and that some display options can be burdensome, it seemed fitting that cart vars will expire when not actively used.
  • lines changed 2, context: html, text, full: html, text
    Angie saw a compiler error that I didn't. Thus I correct an invalid assert.
  • lines changed 107, context: html, text, full: html, text
    More experimentation on buttons/controls with Brooke for haplotypes. At this point, we agree to leave things as they are until a wider audience has a chance to weigh in.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    First check-in of the bluk of code for geneAlleles tool and hgGene's 'Gene Haplotype Alleles' section. This haplotype code, still evolving, relies upon vcf files (1000 Genomes phase 1) to discover sets of individual variants within a protein coding gene model that are segregating as distinct haplotypes. Ongoing work is expected to strengthen scoring routines for better highlighting of unexpected results. Haplotypes are currently only built for protein coding genes, but can certainly be expanded to cover other gene models and indeed, an region of the genome.
• src/inc/bits.h
  • lines changed 11, context: html, text, full: html, text
    Added a couple useful functions that will be needed by haplotypes code.
• src/inc/vcfBits.h
  • lines changed 38, context: html, text, full: html, text
    Changes in preparation for checking in haplotypes code.
• src/lib/bits.c
  • lines changed 71, context: html, text, full: html, text
    Added a couple useful functions that will be needed by haplotypes code.
• src/lib/vcfBits.c
  • lines changed 233, context: html, text, full: html, text
    Changes in preparation for checking in haplotypes code.