Commits for angie

v303_base to v304_preview (2014-07-21 to 2014-07-28) v304

• SNP tracks have an option to include orthologous chimp allele andobserved alleles in the item names. So far, this option has been
  offered only when there is an ortho table for the SNP track, and
  alleles have been included only when a chimp allele is found.
  However, for comparison with other annotations, it is useful to
  see observed alleles even when chimp alleles aren't available.
  Now, if there is no ortho table, the option to include just observed
  alleles is given. If enabled, then when there is no ortho table, or
  no ortho allele for a particular SNP, observed alleles are added to
  the item name.
  
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgTracks/variation.c - lines changed 31, context: html, text, full: html, text
• trackDb and friends for snp141* tracks. refs #13309
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp141.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp141.shared.html - lines changed 467, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp141Common.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp141Flagged.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp141Mult.html - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 121, context: html, text, full: html, text
• For SNPs tracks option to append alleles to the rs# ID in the item name, by default show alleles on the + strand of reference.If a user still wants to see alleles on dbSNP's arbitrary and unstable strand, there's a new option to do so.
  refs #13694
  
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgTracks/variation.c - lines changed 54, context: html, text, full: html, text