v104-final

• Angie continues to work on performance enhancements in lib/hgFind.c:
  • She has added a grepIndex setting to hgFindSpec, in use in findMrnaKeys and findRefGenes.
  • She has added a organismID hash to findHitsToTables, in use addMrnaPositionTable
  • mrnaAligns now has a count(*) query instead of a value query
• Angie also made a performance improvement to lib/hdb.c to hash chromInfo entries incrementally as they are requested.
• Mark has made numerous changes:
  • Generalize mapping of ccds to other genes; link details of kg, mgc, refseq and ensembl (50+ new lines in hgc.c, 50+ changed lines in hgc.c, new utility src/hg/makeDb/genbank/src/ccds/mkCcdsGeneMap.c)
  • Made ccds details page that has access to protein; change mapping between ccds and kg (50 lines in hgGene.c, 300 lines in hgc.c, new program src/hg/lib/chromBins.c)
  • Use hGetMinIndexLength to determine number of characters of the chrom to use in building indexes, added to src/hg/lib/genePred.c
  • Simplified pipeline interface and fixed bug that left pipes open in parent (src/lib/pipeline.c).
  • enable all warnings in src/lib/makefile
  • add option to align-genbank to continue at the copy phase
  • genbank: make creating download into a separate task
  • numerous fixes for warnings
• Jim has made extensive additions to paraFlow.
• Jim also added botDelays in hgTables.
• Hiram continues to work on mm6.
• Hiram also made an edit to hgLoadPsl for .gz input.
• Brian added mafAddIRow.c, a program to add syntenic relationship information to maf files (documented in src/lib/maf.doc).
• Brian also added a hideTracks cgi var to hgTracks (requested via the mailing list).
• Brian also noticed and fix a bug in the protein track code.
• Donna changed 2000+ lines in 50+ files.
• Rachel is working on zebrafish STS markers.
• Kate continues to work on Gencode.
• Robert reversed a commit in src/hg/makeDb/trackDb/trackDb.ra.