v122-preview

New things:

• Jim is writing hgConvert.
• Jim added an index option to chainSort.
• Jim worked out a scheme to download a lot of gensat data, including new util wgetMd5.c.
• Jim added 2 new functions to xap.c.
• Jim added a column option to lineFileSplit.
• Mark has rewritten pslFromAlign in psl.c.
• Mark has a new util gtfToGenePred.
• Mark has edits to geneBounds/clusterGenes.c to fix bug with combining -flatBed and -cds, and to make conflict detection optional rather than default.
• Kate has extracted the ENCODE trackDb.ra descriptions in include files.
• Brian added the ability to specify "loose" or "medium" gap costs in gapCalc.c. axtChain.c now requires that gap costs be specified.
• Brian extended mafAddIRows.c to handle Ns.
• Hiram added the chainLinearGap option to doBlastzChainNet.
• Galt wrote a utility genePredToFakePsl.

Edits:

• Jim has edits to autoXml.
• Jim incorporated QA feedback to hgVisiGene.

Data:

• Hiram rescored the mm7 blastz runs. He is also working on the 17-way alignment.
• Angie completed droYak2.
• Andy created new mouse liftOver chains.
• Andy did RIKEN CAGE tracks for mm5 and mm6.
• Fan completed mm7 KG/GS/PB.
• Rachel is working on danRer3 self blastz and canFam1 BAC Ends.

Ongoing:

• Belinda is working on the human mutation track.
• Heather is working on snpLoad.c.