Commits for angie

v319_base to v320_preview (2015-07-13 to 2015-07-20) v320

• Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
  assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
  orangutan and macaque & extraction of their nucleotide at that position).
  refs #15493
  
  Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
  identifiers in all.joiner.
  refs #3606
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 114, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp144.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp144.shared.html - lines changed 470, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp144Common.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp144Flagged.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/snp144Mult.html - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 107, context: html, text, full: html, text
  • src/hg/utils/automation/categorizeSnps.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnp.pl - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnpMaskSequence.pl - lines changed 271, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnpOrthoAlleles.pl - lines changed 309, context: html, text, full: html, text
  • src/hg/utils/automation/joinOrthoAlleles.csh - lines changed 54, context: html, text, full: html, text
  • src/hg/utils/automation/snpAddTGPAlleleFreq.pl - lines changed 30, context: html, text, full: html, text
• Adding -s (silent) to curl so it doesn't report speed to stderr when we run make > /dev/null.
  
  • src/hg/hgMirror/makefile - lines changed 1, context: html, text, full: html, text
• Adding Data Integrator to list of destinations from the Manage Custom Tracks
  page. Since there are now 4 destinations, instead of having one button for
  each, use a menu to select the destination and a single 'go' button.
  Align the 'add custom tracks' button with the new menu.
  refs #15517
  
  • src/hg/hgCustom/hgCustom.c - lines changed 86, context: html, text, full: html, text