v105-preview

• Kate has made a number of GUI changes:
  • Add base-level display of additional gap and break annotations in multiple alignments
  • Add red break indicator to medium zoom level
  • Draw double and single-chain lines between pairwise alignments zoomed out
  • Change break indicator to blue
  • Change base-level chain indicator to '=' from 'o'
  • Add double/single lines in gaps of multiple alignment display (from just above base-level to 1Mbp)
• Andy has completed the restriction enzyme track (it is in the QA push queue).
• Hiram has completed cytoBand and STS markers for mm6.
• Hiram is working on the Conservation track.
• Fan has completed Known Genes, Affy tracks and Gene Sorter for mm6.
• Fan added a new utility kgXref2.
• Mark has implemented a repeat match filter in pslCDnaFilter.
• Mark has added the building of the grepIndex.
• Mark fixed a number of warnings.
• Heather added a sleep to hgTablesTest, and also added error checking and retries.
• Angie has completed a basic browser on droSim1 and passed off to QA.
• Angie added nfsNoodge to doBlastzChainNet.pl.
• Angie has some additions to apiMel2.
• Donna has 3000 lines changed in 60 files.
• Jim is continuing to work on paraFlow.
• Kate is continuing to work with ENCODE data.