Commits for angie

v289_preview to v289_preview2 (2013-08-26 to 2013-09-02) v289

• Building snp138*. Initial config should not have ignoreDbSnpContigsWhatever. The first run will complain about not finding patch contigs. Use that run's suggestedLft as the list of contigs to ignore, after inspecting it first. It would be better to use a copy of it just in case somehow it gets overwritten with even more unfound contigs if we re-run or something... because the overwritten version would have only the newly unfound contigs.
  • src/hg/makeDb/doc/hg19.txt - lines changed 474, context: html, text, full: html, text
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnp.pl - lines changed 1, context: html, text, full: html, text
• dbSNP has made yet another change to allele frequency info in snp138:now if there are no non-1000Genomes allele freq/counts, but there are
  1000Genomes freq/counts, the 1000Genomes freq/counts are copied into
  the otherwise non-1000Genomes table (SNPAlleleFreq_TGP data are copied
  into SNPAlleleFreq). Detect those cases of copying and don't add the
  duplicated freq/counts. refs #11438
  
  • src/hg/utils/automation/snpAddTGPAlleleFreq.pl - lines changed 84, context: html, text, full: html, text
• Oops, forgot to check self->notSorted in chunking queries. fixes #11625
  • src/hg/lib/annoStreamDb.c - lines changed 7, context: html, text, full: html, text
• Adding snp138 to all.joiner. refs #11438
  • src/hg/makeDb/schema/all.joiner - lines changed 12, context: html, text, full: html, text
• Don't hardcode the path of true as /bin/true; not the same on all systems.
  • src/hg/checkTableCoords/tests/makefile - lines changed 1, context: html, text, full: html, text