Commits for angie

v274_base to v275_preview (2012-10-09 to 2012-10-16) v275

• HTML-encode VCF alternate alleles in case they're symbolic like "<DEL>" (but don't encode twice :).
  • src/hg/hgc/vcfClick.c - lines changed 9, context: html, text, full: html, text
• Track #7964 (1000 Genomes Phase 1 Variant Calls): Reloaded -- thedownload files have been updated with new dbSNP and dbVar IDs.
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 30, context: html, text, full: html, text
• Fixing liftOver of bedPlus, copy-paste-forget-edit bug introduced inb224dbbd -- important arguments of liftOverBedPlus were discarded,
  like bedPlus(!), hasBin and tabSep.
  
  • src/hg/lib/liftOver.c - lines changed 1, context: html, text, full: html, text
• Small update to tgpPhase1 description: paper has been accepted.
  • src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html - lines changed 1, context: html, text, full: html, text
• hgLoadSqlTab: check NULL to avoid crashing on SQL files that don't include "(" at the end of their "CREATE TABLE" line.
  • src/hg/makeDb/hgLoadSqlTab/hgLoadSqlTab.c - lines changed 1, context: html, text, full: html, text
• Check for NULL in errAbort arguments, or else we can SEGV and see blank screen.
  • src/hg/lib/customFactory.c - lines changed 2, context: html, text, full: html, text
• Fix for strict compiler warning: warn() needs a proper format string, not char * variable.
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text