Commits for hiram

v294_preview2 to v294_base (2014-01-06 to 2014-01-13) v294

• ignore the noSplit arguments to make it become the default refs #11681
  • src/hg/makeDb/hgLoadOut/hgLoadOut.c - lines changed 7, context: html, text, full: html, text
• up to date repeat masker procedures, trf simple repeats and genscan refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 688, context: html, text, full: html, text
• adding other genomes found on the RR for completeness refs #10272
  • src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab - lines changed 14, context: html, text, full: html, text
• add url to animalQtl refs #10954
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 4, context: html, text, full: html, text
• animalQtl reloading refs #10954
  • src/hg/makeDb/doc/galGal4.txt - lines changed 6, context: html, text, full: html, text
• rerunning repeat masking refs #11682
  • src/hg/makeDb/doc/hg38.txt - lines changed 83, context: html, text, full: html, text
• liftOver to hg38 done refs #11681
  • src/hg/makeDb/doc/hg19.txt - lines changed 26, context: html, text, full: html, text
• move the rmsk experments to experimental track group refs #11681
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 6, context: html, text, full: html, text
• adding par and centromere tracks refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 59, context: html, text, full: html, text
• documentation for the centromere track refs #11681
  • src/hg/makeDb/trackDb/human/hg38/centromeres.html - lines changed 6, context: html, text, full: html, text
• adding RepeatMasker cross-match documentation refs #11681
  • src/hg/makeDb/trackDb/human/hg38/rmskCM.html - lines changed 105, context: html, text, full: html, text
• update the featureBits and add the class summary refs #11681
  • src/hg/makeDb/trackDb/human/hg38/rmskBlastn.html - lines changed 26, context: html, text, full: html, text
• add the class summary refs #11681
  • src/hg/makeDb/trackDb/human/hg38/rmskCM.html - lines changed 25, context: html, text, full: html, text
• add the class summary refs #11681
  • src/hg/makeDb/trackDb/human/hg38/rmskGenbank.html - lines changed 25, context: html, text, full: html, text
• the alternate/haplotype sequence lastz chain net psl track refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 159, context: html, text, full: html, text
• add directory safety checks as it starts refs #9104
  • src/product/scripts/kentSrcUpdate.sh - lines changed 15, context: html, text, full: html, text
• adding alternate haplotype sequences chain net psl locations track refs #11681
  • src/hg/makeDb/trackDb/human/hg38/altSequences.ra - lines changed 91, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 20, context: html, text, full: html, text
• done with rmskHmmer and added hg38.contigs.2bit build refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 90, context: html, text, full: html, text
• adding HMMER rmsk documentation refs #11681
  • src/hg/makeDb/trackDb/human/hg38/rmskCM.html - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/trackDb/human/hg38/rmskHmmer.html - lines changed 127, context: html, text, full: html, text
• add repeat masker analysis refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 56, context: html, text, full: html, text
• need to use 32Gb and 4 CPU limits on HMMER refs #11681
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 2, context: html, text, full: html, text
• preparing for GRCh38/hg38 genbank run refs #11681
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 25, context: html, text, full: html, text
• new convention for location of bbi files, in bbi/tableName/... refs #11681
  • src/hg/utils/automation/makeGenomeDb.pl - lines changed 8, context: html, text, full: html, text
• fixup gc5BaseBw bbi directory path, and running cpgIslands on contig sequence refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 98, context: html, text, full: html, text
• v294 final build refs #12191
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v294
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text