Commits for angie

v306_preview to v306_preview2 (2014-09-08 to 2014-09-15) v306

• Changes to snpNcbiToUcsc to handle b141 on hg19 and hg38:- When checking range{I,D,S}* locTypes, use strlen(refNCBI) as length only if
  refNCBI contains only nucleotides.
  - Checking for overlapping variants at the same location (checkCluster ->
  DuplicateObserved, MixedObserved) used to be limited to insertions because
  those are easier to check. Now we check all variants that have
  all-nucleotide observed. Libified some code from hgTracks that can
  reverse-complement a slash-separated string of alleles, e.g. G/T -> A/C,
  -/AG -> -/CT.
  - SNP IDs are getting too huge (and sparse) to use as indexes into a
  statically allocated array; use a hash.
  - Erroneous NULL frequencies in dbSNP's SNPAlleleFreq need to be detected
  and ignored.
  refs #13309
  
  • src/hg/hgTracks/variation.c - lines changed 20, context: html, text, full: html, text
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 123, context: html, text, full: html, text
  • src/inc/dnautil.h - lines changed 5, context: html, text, full: html, text
  • src/lib/dnautil.c - lines changed 35, context: html, text, full: html, text
• Changes to support dbSNP b141, released on both hg19 and hg38:- Support multiple assemblies of the same organism in a single build.
  - Support strange one-off orgDir like human_9606_b141_GRCh37p13.
  - Added 'filter' step to extract snpNNN{Common,Mult,Flagged} sets and load tables.
  - Added coding step to make snpNNNCodingDbSnp table.
  refs #13309
  
  • src/hg/utils/automation/doDbSnp.pl - lines changed 101, context: html, text, full: html, text
• SNPs(141) tracks (dbSNP b141, released for both hg19 and hg38).refs #13309
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 531, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38.txt - lines changed 542, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 12, context: html, text, full: html, text
• Removing snp141Mult track from hg19/trackDb.ra... there are no Mults in hg19 snp141!refs #13309
  
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 3, context: html, text, full: html, text
• typo fix
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 4, context: html, text, full: html, text
• Removing dead code for "useTarg" (#ifndef'd out with BRANEY_SAYS_USETARG_IS_OBSOLETE).
  • src/hg/hgTracks/wigMafTrack.c - lines changed 64, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 36, context: html, text, full: html, text
• Added eboVir2.multiz49wayStrainNames, which is multiz49way.maf with strain names from http://epidemic.bio.ed.ac.uk/ebolavirus_sequences
  • src/hg/makeDb/doc/eboVir2/multizLabels.txt - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49wayStrainNames.ra - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text
• Added a couple VCF tracks from Gire et al (99 samples from 78 patients,variants called with other Zaire-clade ebola viruses).
  
  • src/hg/makeDb/doc/eboVir2/gire.txt - lines changed 109, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/gireZebov.html - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 14, context: html, text, full: html, text
• Making gireZebov visible by default.
  • src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra - lines changed 1, context: html, text, full: html, text