File Changes for hiram

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

• src/hg/altSplice/altSplice/orthoSplice.c
  • lines changed 1, context: html, text, full: html, text
    remove useless extra parentheses refs #12209
• src/hg/checkTableCoords/checkTableCoords.c
  • lines changed 8, context: html, text, full: html, text
    remove always false if() statement due to unsigned int compare to < 0 refs #12209
• src/hg/genePredCheck/genePredCheck.c
  • lines changed 1, context: html, text, full: html, text
    initialize variable to avoid compiler complaint refs #12209
• src/hg/hgTables/intersect.c
  • lines changed 1, context: html, text, full: html, text
    eliminate useless compare of an unsigned int with < 0 refs #12209
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 5, context: html, text, full: html, text
    fixup potential use of unset variable and better localize variables refs #12209
• src/hg/hgTracks/cytoBandTrack.c
  • lines changed 1, context: html, text, full: html, text
    eliminate a useless self to self assignment statement refs #12209
• src/hg/hgTracks/factorSource.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/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    adding cpgIslandExtUnmasked track handler refs #11681
• src/hg/hgTracks/variation.c
  • lines changed 7, context: html, text, full: html, text
    fixup enum type casts refs #12209
• src/hg/hgTracks/variation.h
  • lines changed 1, context: html, text, full: html, text
    sumValues can be negative now using an int instead of unsigned refs #12209
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 1, context: html, text, full: html, text
    fixup broken if() statement, was always drawing chains where it should not refs @12209
• src/hg/hgTracks/wigTrack.c
  • lines changed 4, context: html, text, full: html, text
    fixup enum types conversions and eliminate useless duplicate parentheses refs #12209
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    eliminate always TRUE condition of if() statement refs @12209
• src/hg/lib/ggGraph.c
  • lines changed 1, context: html, text, full: html, text
    remove useless self assignment 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/snp125Ui.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/wiggleCart.c
  • lines changed 2, context: html, text, full: html, text
    casting enum to avoid compile warnings refs #12209
• src/hg/liftAgp/liftAgp.c
  • lines changed 2, context: html, text, full: html, text
    fixup argument declaration to match actual use refs #12209
• src/hg/liftUp/liftUp.c
  • lines changed 1, context: html, text, full: html, text
    clarify genepred types in usage message refs #11681
• src/hg/makeDb/doc/hg38.txt
  • lines changed 55, context: html, text, full: html, text
    cpgIslands done blat server on default position set refs #11681
  • lines changed 70, context: html, text, full: html, text
    genscan track done on contig hard masked sequence refs #11681
• src/hg/makeDb/outside/allenBrain/allenCollectSeq/allenCollectSeq.c
  • lines changed 1, context: html, text, full: html, text
    remove bad ascii character from ascii string refs #12209
• src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c
  • lines changed 1, context: html, text, full: html, text
    fix empty if statement, path never taken before refs #12209
• src/hg/makeDb/schema/all.joiner
  • lines changed 10, context: html, text, full: html, text
    checking in hg38 definitions refs #11681
  • lines changed 3, context: html, text, full: html, text
    correctly avoiding checks on wormBaseId flyBaseGeneId and sgdCodingId on hg38 refs #11681
• src/hg/makeDb/trackDb/human/hg38/altSequences.ra
  • lines changed 2, context: html, text, full: html, text
    setting default track visibilities refs #11681
• src/hg/makeDb/trackDb/human/hg38/cpgIslandSuper.html
  • lines changed 63, context: html, text, full: html, text
    now have a superTrack for two CpG Island tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/crossMatchUnique.html
  • lines changed 12, context: html, text, full: html, text
    description pages for the HMMER vs. Cross-Match unique tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 21, context: html, text, full: html, text
    mention sections to fill in refs #11706
• src/hg/makeDb/trackDb/human/hg38/hmmerUnique.bed
  • lines changed 12, context: html, text, full: html, text
    description pages for the HMMER vs. Cross-Match unique tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 26, context: html, text, full: html, text
    now have a superTrack for two CpG Island tracks refs #11681
  • lines changed 29, context: html, text, full: html, text
    setting default track visibilities refs #11681
• src/hg/mouseStuff/lavToPsl/lavToPsl.c
  • lines changed 2, context: html, text, full: html, text
    correct cloneString qName and tName into psl structure to avoid free problem refs #12352
• src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.bed.gz
  • lines changed 0, context: html, text, full: html, text
    add test cases for bug refs #12502
• src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.psl.gz
  • lines changed 0, context: html, text, full: html, text
    add test cases for bug refs #12502
• src/hg/mouseStuff/lavToPsl/tests/input/redmine12502.lav.gz
  • lines changed 0, context: html, text, full: html, text
    add test cases for bug refs #12502
• src/hg/mouseStuff/lavToPsl/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    add test cases for bug refs #12502
• src/hg/near/hgNearTest/hgNearTest.c
  • lines changed 5, context: html, text, full: html, text
    fixup initialization of variable before use and localize variables refs #12209
• src/hg/txGraph/txOrtho/txOrtho.c
  • lines changed 2, context: html, text, full: html, text
    remove useless extra parentheses 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/lib/cheapcgi.c
  • lines changed 6, context: html, text, full: html, text
    casting enum to avoid compile warnings refs #12209
• src/product/scripts/README.trashCleaning
  • lines changed 17, context: html, text, full: html, text
    indicate that a simple system could be used refs #11957
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v295 preview1 refs #12352
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 11, context: html, text, full: html, text
    correctly copy binaries from hgwdev to hgwbeta after they are build refs #12352