v120-preview

New things:

• Kate has edits to hgTracks for composite tracks
• Chuck has edits to hgTracks to fix problems with affyTxnPhase2 track (some backed out)
• Galt added new library code: mime.c, quickHeap.c
• Robert Baertsch has edits to gbArchaeGenome and hgc for Archaea genome
• Fan added fuzzy search on Known Genes description to hgFind.c
• Todd Lowe added Perl scripts to automatically create microbial genome browsers (8000 lines)
• Craig (lowec) - new function twoBitSeqSizeNoNs in twoBit.c
• Mark has a new util mafFetch
• Mark added an interface to get pipeline input from a memory buffer
• Mark added support for files larger than 4GB to faSplit.c
• Mark has edits to genePredToMafFrames to handle genes that map to multiple locations
• Matej (lexa) - edits to blatz
• Jim added new utils: maxEachRow, minEachRow
• Jim has additions to jksql: sqlQuickNonemptyString, sqlQuickNumList
• Jim made an addition to common.c: differentStringNullOk()
• Heather added perf/hgTracksRandom.c
• Jim added a new feature to textHistogram

Bug fixes:

• Galt has edits to chainMergeSort.c
• Andy Pohl had a fix to gbArchaeGenome.c.
• Robert Baertsch has a bug fix in hg/lib/spDb.c.
• Daryl has edits to the LD track (backed out in v120 final)
• Fan has edits to protein scripts
• Hiram cleaned up sageVisVGI dir
• Mark has edits to mafToPsl

Data:

• Kate had lots of ENCODE trackDb edits.
• Andy Pohl is working on red flour beetle (triCas2)
• Rachel danRer3: added tetNig1 & monDom2 net/chain tracks
• Rachel added danRer3 net/chain tracks to tetNig1 & monDom2,
• Hiram - mm7 additions, stricter filtering for mm6 STS markers

Ongoing:

• Brian continues to work on the ancestor reconstruction
• Jim has edits to VisiGene