v156-final - 3 Apr. 2007    (Pairings)

Code changes:

• Added functionality to cgapSageFind.c, updated cgapSage.c to store SNP info. (Andy)
• Reworked partial aligment display to fix bug: edges of region were colored as alignment gaps even if they shouldn't be. (Angie)
• Added a couple gates to hgSession.c with wikiLinkEnabled() to make prevent errors when hg.conf does not have wiki settings. (Angie)
• Updated mouseStuff/simpleChain.c to be 64-bit compatible. (Brian)
• Fixed ratStuff/magAddIRows.c to not use memory-intensive binKeeper library. (Brian)
• Added routine to maf.c/maf.h to find all components. (Brian)
• Added ellipse routines to psGfx.c/.h, common.ps/.pss. (Brian)
• Updated several protein modules to accommodate KGIII. (Fan)
• Updated KEGG links in hgGene/pathways.c. (Fan)
• Updated program for building knownGeneList to accommodate KGIII, exclude noncoding genes. (Fan)
• Split hgNetDist.c (GS) into hgNetDist.c and hgLoadNetDist.c to facilitate faster incremental kg3 building. (Galt)
• Added utility to hgNetDist/hprdP2p.c (GS) for processing HPRD PPI, complexes in flat file format to make the p2p input for hgNetDist. (Galt)
• Added utility to knownToHprd.c (GS) to create knownToHprd. (Galt)
• Added correct mapping to psl in knownToVisiGene.c. (Galt)
• Upgraded the java version to jdk1.5.0_10. (Heather)
• Added track handler for delHinds2. (Heather)
• Fixed bug in hgFind.c -- match from subtrack needs to send parent to open track. (Heather)
• Added hTrackIsSubtrack() and hGetParent() to hdb.c. (Heather)
• Ongoing KGIII work. (Jim)
• Modified GS pfam column use knownToPfam (and sangerToPfam etc) rather than taking a long trip through the proteome database that sometimes ended up badly. (Jim)
• Modified GS to clear settings when user switches assemblies as well as organisms. (Jim)
• Cleaned up various issues detected by GCC 4.3, removed explicit use of HOME in several makefiles (use common.mk defines instead), fixed portability issues. (Mark)
• Modified chopByChar in lib/common.c to allow NULL output array to get number of columns that would be produced, just like the other chop functions. (Mark)

Data changes:

• Updated cgapSage table to store SNP info. (Andy)
• Added human proteins track to mm8. (Brian)
• Rebuilt knownGeneList for hg18. (Fan)
• Work on cnpSharp2, cnpIafrate delHinds2. (Heather)
• Ongoing work on braFlo1. (Hiram)
• Ongoing worm-building work. (Hiram)
• Corrected multiz annotations on fr2, gasAcu1, mm8. (Hiram)
• Ongoing KGIII work. (Jim)
• Added altEvent track on hg18. (Jim)
• Ongoing work on hg18 28-way alignment. (Kate)
• Obtained new ENCODE data submissions from Yale and Gencode. (Kate)
• Cleaned up zebrafish. (Rachel)
• Added nscanGene to equCab1. (Robert)