Commits for hiram

v294_base to v295_preview (2014-01-13 to 2014-01-20) v295

• adding cpgIslandExtUnmasked track handler refs #11681
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
• now have a superTrack for two CpG Island tracks refs #11681
  • src/hg/makeDb/trackDb/human/hg38/cpgIslandSuper.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 26, context: html, text, full: html, text
• setting default track visibilities refs #11681
  • src/hg/makeDb/trackDb/human/hg38/altSequences.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 29, context: html, text, full: html, text
• correctly copy binaries from hgwdev to hgwbeta after they are build refs #12352
  • src/utils/qa/weeklybld/doNewBranch.csh - lines changed 11, context: html, text, full: html, text
• correct cloneString qName and tName into psl structure to avoid free problem refs #12352
  • src/hg/mouseStuff/lavToPsl/lavToPsl.c - lines changed 2, context: html, text, full: html, text
• remove useless self assignment refs #12209
  • src/hg/lib/ggGraph.c - lines changed 1, context: html, text, full: html, text
• remove useless extra parentheses refs #12209
  • src/hg/altSplice/altSplice/orthoSplice.c - lines changed 1, context: html, text, full: html, text
• fixup potential use of unset variable and better localize variables refs #12209
  • src/hg/hgTablesTest/hgTablesTest.c - lines changed 5, context: html, text, full: html, text
• fixup argument declaration to match actual use refs #12209
  • src/hg/liftAgp/liftAgp.c - lines changed 2, context: html, text, full: html, text
• remove bad ascii character from ascii string refs #12209
  • src/hg/makeDb/outside/allenBrain/allenCollectSeq/allenCollectSeq.c - lines changed 1, context: html, text, full: html, text
• fix empty if statement, path never taken before refs #12209
  • src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c - lines changed 1, context: html, text, full: html, text
• remove useless enum compare to less than zero never possible refs #12209
  • src/hg/lib/snp125Ui.c - lines changed 1, context: html, text, full: html, text
• fixup initialization of variable before use and localize variables refs #12209
  • src/hg/near/hgNearTest/hgNearTest.c - lines changed 5, context: html, text, full: html, text
• mention sections to fill in refs #11706
  • src/hg/makeDb/trackDb/human/hg38/description.html - lines changed 21, context: html, text, full: html, text
• remove useless extra parentheses refs #12209
  • src/hg/txGraph/txOrtho/txOrtho.c - lines changed 2, context: html, text, full: html, text
• remove always false if() statement due to unsigned int compare to < 0 refs #12209
  • src/hg/utils/gapToLift/gapToLift.c - lines changed 3, context: html, text, full: html, text
• remove always false if() statement due to unsigned int compare to < 0 refs #12209
  • src/hg/checkTableCoords/checkTableCoords.c - lines changed 8, context: html, text, full: html, text
• initialize variable to avoid compiler complaint refs #12209
  • src/hg/genePredCheck/genePredCheck.c - lines changed 1, context: html, text, full: html, text
• casting enum to avoid compile warnings refs #12209
  • src/lib/cheapcgi.c - lines changed 6, context: html, text, full: html, text
• casting enum to avoid compile warnings refs #12209
  • src/hg/lib/ggTypes.c - lines changed 5, context: html, text, full: html, text
• casting enum to avoid compile warnings refs #12209
  • src/hg/lib/wiggleCart.c - lines changed 2, context: html, text, full: html, text
• description pages for the HMMER vs. Cross-Match unique tracks refs #11681
  • src/hg/makeDb/trackDb/human/hg38/crossMatchUnique.html - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hmmerUnique.bed - lines changed 12, context: html, text, full: html, text
• cpgIslands done blat server on default position set refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 55, context: html, text, full: html, text
• indicate that a simple system could be used refs #11957
  • src/product/scripts/README.trashCleaning - lines changed 17, context: html, text, full: html, text
• eliminate useless compare of an unsigned int with < 0 refs #12209
  • src/hg/hgTables/intersect.c - lines changed 1, context: html, text, full: html, text
• eliminate a useless self to self assignment statement refs #12209
  • src/hg/hgTracks/cytoBandTrack.c - lines changed 1, context: html, text, full: html, text
• fix a broken if() statement that allowed always TRUE behavior refs #12209
  • src/hg/hgTracks/factorSource.c - lines changed 1, context: html, text, full: html, text
• fixup enum types conversions and eliminate useless duplicate parentheses refs #12209
  • src/hg/hgTracks/wigTrack.c - lines changed 4, context: html, text, full: html, text
• fixup broken if() statement, was always drawing chains where it should not refs @12209
  • src/hg/hgTracks/wigMafTrack.c - lines changed 1, context: html, text, full: html, text
• fixup enum type casts refs #12209
  • src/hg/hgTracks/variation.c - lines changed 7, context: html, text, full: html, text
• eliminate always TRUE condition of if() statement refs @12209
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text
• clarify genepred types in usage message refs #11681
  • src/hg/liftUp/liftUp.c - lines changed 1, context: html, text, full: html, text
• add test cases for bug refs #12502
  • src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.bed.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.psl.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/lavToPsl/tests/input/redmine12502.lav.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/lavToPsl/tests/makefile - lines changed 7, context: html, text, full: html, text
• genscan track done on contig hard masked sequence refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 70, context: html, text, full: html, text
• checking in hg38 definitions refs #11681
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text
• correctly avoiding checks on wormBaseId flyBaseGeneId and sgdCodingId on hg38 refs #11681
  • src/hg/makeDb/schema/all.joiner - lines changed 3, context: html, text, full: html, text
• sumValues can be negative now using an int instead of unsigned refs #12209
  • src/hg/hgTracks/variation.h - lines changed 1, context: html, text, full: html, text
• v295 preview1 refs #12352
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text