Commits for angie

v292_base to v293_preview (2013-11-11 to 2013-11-18) v293

• Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
  LRGs are frozen reference sequences for a particular gene plus some
  upstream and downstream sequence. They are intended to provide a
  stable coordinate system for gene annotations that won't change
  with every new genome assembly, but can be mapped to each genome
  assembly. Since there is a lot of metadata associated with each
  region, I made LRG Regions a bigBed 12 + with fields describing
  mismatches and indels, so that PSL can be derived from the bigBed
  and the original LRG sequence can be reconstructed using genome
  assembly sequence and the mismatch/indel info. hgTracks shows
  differences and LRG insertions into the reference assembly using
  the cds.c baseColor code. (LRG deletions from the reference appear
  as gaps, which we get for free with bed12 info).
  For LRG Transcripts, I found the genePred codon-coloring code
  inadequate for showing an insertion into hg19 (or even mismatches),
  so instead of genePred I ended up using PSL + sequence, more like
  the mRNA track representation and display.
  
  • src/hg/genePredToFakePsl/genePredToFakePsl.c - lines changed 32, context: html, text, full: html, text
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/cds.c - lines changed 26, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/lrgTrack.c - lines changed 62, context: html, text, full: html, text
  • src/hg/hgTracks/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 108, context: html, text, full: html, text
  • src/hg/hgc/hgc.h - lines changed 12, context: html, text, full: html, text
  • src/hg/hgc/lrgClick.c - lines changed 248, context: html, text, full: html, text
  • src/hg/hgc/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/hdb.h - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 7, context: html, text, full: html, text
  • src/hg/inc/lrg.h - lines changed 109, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 49, context: html, text, full: html, text
  • src/hg/lib/lrg.as - lines changed 25, context: html, text, full: html, text
  • src/hg/lib/lrg.c - lines changed 480, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 70, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrg.html - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrgTranscriptAli.html - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/parseLrgXml.pl - lines changed 221, context: html, text, full: html, text
  • src/hg/utils/lrgToPsl/lrgToPsl.c - lines changed 51, context: html, text, full: html, text
  • src/hg/utils/lrgToPsl/makefile - lines changed 3, context: html, text, full: html, text
  • src/inc/hash.h - lines changed 4, context: html, text, full: html, text
  • src/lib/hash.c - lines changed 19, context: html, text, full: html, text
• Updated descriptions of LRG tracks with info from Fiona Cunningham at EBI.refs #11863
  
  • src/hg/makeDb/trackDb/human/lrg.html - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrgTranscriptAli.html - lines changed 9, context: html, text, full: html, text
• Added md5HexForString.
  • src/inc/md5.h - lines changed 3, context: html, text, full: html, text
  • src/lib/md5.c - lines changed 17, context: html, text, full: html, text
• isAllDna has a condition that surprised me (returns FALSE if size is 1),so I added isAllNt which has the behavior I expected.
  
  • src/inc/dnautil.h - lines changed 5, context: html, text, full: html, text
  • src/lib/dnautil.c - lines changed 15, context: html, text, full: html, text
• Added comment method to annoFormatter.
  • src/hg/lib/annoFormatVep.c - lines changed 13, context: html, text, full: html, text
  • src/inc/annoFormatter.h - lines changed 3, context: html, text, full: html, text
  • src/lib/annoFormatTab.c - lines changed 10, context: html, text, full: html, text
• Work in progress for #11460 (paste/upload variant input options...):adding an option for user to paste/upload variant identifiers which
  will be translated into a sorted list of vcfRecords.
  
  Currently we recognize only rs# IDs. I was considering adding
  dbVar IDs, but those could come from multiple sources (DGV, ClinVar,
  ISCA) so I'm not sure.
  
  Treating all symbolic/named alleles as deletions... non-ideal,
  but fortunately those are a small minority in dbSNP.
  
  Next: recognize HGVS IDs.
  
  The grander vision of #11460 includes accepting VEP input format
  and VCF, but I think those should be new SELECT options so we don't
  get into quagmire of guessing format.
  
  • src/hg/hgVai/hgVai.c - lines changed 394, context: html, text, full: html, text
  • src/hg/js/hgVarAnnogrator.js - lines changed 11, context: html, text, full: html, text
  • src/hg/lib/gpFx.c - lines changed 9, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 6, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 24, context: html, text, full: html, text