v108-preview

• Fan is continuing to work on KG. He has 300+ lines added/changed in makeHg17.doc. He has also created makeProteins050415.doc. He has integrated support for variant splice proteins.
• Hiram, Angie, Kate and Heather are loading ENCODE tracks. Hiram is finalizing the bedGraph format.
• Angie also loaded SGP Genes for mm6 and multiz9way for dm2.
• Angie reloaded SGP Genes for mm5 (chrX was missing).
• Mark added -joinContained option to clusterGenes.
• Mark added -idMatch option to overlapSelect.
• Mark added option to chainToPsl to set repMasked count.
• Mark rewrote pslSwap to simplify and fix a bug.
• Mark fixed a bug in pslMap regarding reverse strand alignments.
• Mark added an option to getRna to output peptides.
• Rachel is working with BAC Ends for danRer1 and danRer2.
• Robert editted the hgc display for ESTs.
• Andy added an Exonerate track for apiMel2.