Commits for tdreszer
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v283_preview to v283_preview2 (2013-04-23 to 2013-04-30) v283
- Added a couple useful functions that will be needed by haplotypes code.
- Changes in preparation for checking in haplotypes code.
- Added routines for getting genePred coding DNA and determining coding position. To be used in haplotypes code about to be checked in.
- Added styles for gene haplotype alleles section of hgGene which will soon be checked in.
- src/hg/htdocs/style/HGStyle.css - lines changed 22, 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.
- 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/hg/inc/haplotypes.h - lines changed 274, context: html, text, full: html, text
- src/hg/lib/haplotypes.c - lines changed 3340, context: html, text, full: html, text
- In moving haplotypes to be cart persistent, toggling visibility by class helps.
- src/hg/htdocs/style/HGStyle.css - lines changed 3, 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.
- 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/inc/haplotypes.h - lines changed 10, context: html, text, full: html, text
- src/hg/lib/haplotypes.c - lines changed 206, context: html, text, full: html, text
- Angie saw a compiler error that I didn't. Thus I correct an invalid assert.
- src/hg/lib/haplotypes.c - lines changed 2, context: html, text, full: html, text
- Collapsed 2 button styles into 1 for haplotypes.
- src/hg/htdocs/style/HGStyle.css - lines changed 2, 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/haplotypes.c - lines changed 107, context: html, text, full: html, text
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