File Changes for hiram

v293_preview to v293_preview2 (2013-11-18 to 2013-12-02) v293

• src/hg/hgTables/hal.c
  • lines changed 7, context: html, text, full: html, text
    temporary disable USE_HAL check to verify refs #12119
  • lines changed 7, context: html, text, full: html, text
    remove temporary disable USE_HAL check to verify refs #12119
• src/hg/lib/hgMaf.c
  • lines changed 1, context: html, text, full: html, text
    fix broken if statement refs #12209
• src/hg/lib/imageClone.c
  • lines changed 1, context: html, text, full: html, text
    correctly initialize sizeOne before use refs @12209
• src/hg/lib/jksql.c
  • lines changed 2, context: html, text, full: html, text
    make sure numChanged and numMatched are initialzed properly before use refs #12209
• src/hg/lib/jsHelper.c
  • lines changed 1, context: html, text, full: html, text
    remove redundant semi-colon refs #12209
• src/hg/lib/rmskBed6+10.as
  • lines changed 20, context: html, text, full: html, text
    construct bigBed files for repeat masker result refs #11681
• src/hg/liftOver/tests/makefile
  • lines changed 16, context: html, text, full: html, text
    make sure diff output gets to stderr so we will see the error in email from cron jobs refs #12189
• src/hg/makeDb/doc/ailMel1.txt
  • lines changed 24, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 113, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 20, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 20, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 21, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/falPer1.txt
  • lines changed 0, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/gasAcu1.txt
  • lines changed 13, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/loxAfr3.txt
  • lines changed 13, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/macEug2.txt
  • lines changed 0, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 21, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/mm10.txt
  • lines changed 0, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/myoLuc2.txt
  • lines changed 26, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 79, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/oryLat2.txt
  • lines changed 42, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/makeDb/doc/taeGut2.txt
  • lines changed 23, context: html, text, full: html, text
    complete ensGene lift from taeGut1 with all ens tables refs #10272
• src/hg/makeDb/doc/tetNig2.txt
  • lines changed 22, context: html, text, full: html, text
    bringing genscan up to date on all 100-way involved species refs #10272
• src/hg/utils/automation/HgRemoteScript.pm
  • lines changed 39, context: html, text, full: html, text
    now allow bash scripts in auto jobs and construct bigBed files for repeat masker result refs #11681
• src/hg/utils/automation/configFiles/allMis1.config.ra
  • lines changed 23, context: html, text, full: html, text
    catching up config files refs #10272
• src/hg/utils/automation/configFiles/papHam1.config.ra
  • lines changed 24, context: html, text, full: html, text
    catching up config files refs #10272
• src/hg/utils/automation/doCpgIslands.pl
  • lines changed 2, context: html, text, full: html, text
    also create the bigBed file for use in an assembly hub refs #11770
• src/hg/utils/automation/doGenscan.pl
  • lines changed 8, context: html, text, full: html, text
    prepare bigBed files for assembly hub refs #11681
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 55, context: html, text, full: html, text
    now allow bash scripts in auto jobs and construct bigBed files for repeat masker result refs #11681
• src/hg/utils/automation/rmskBed6+10.pl
  • lines changed 34, context: html, text, full: html, text
    construct bigBed files for repeat masker result refs #11681
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 5, context: html, text, full: html, text
    adding Sperm whale, Straw colored fruit bat, Indian false vampire, Parnell's mustached bat, Burmese python, Amur tiger refs #10272
  • lines changed 1, context: html, text, full: html, text
    adding apiMel4 Honey bee for assembly hub build refs #11681
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 9, context: html, text, full: html, text
    adding Sperm whale, Straw colored fruit bat, Indian false vampire, Parnell's mustached bat, Burmese python, Amur tiger refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 3, context: html, text, full: html, text
    adding Sperm whale, Straw colored fruit bat, Indian false vampire, Parnell's mustached bat, Burmese python, Amur tiger refs #10272
• src/lib/cirTree.c
  • lines changed 2, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    remove redundant set of parens refs #12209
  • lines changed 2, context: html, text, full: html, text
    correctly size 8 byte array for swapping routines refs @12209
• src/lib/elmTree.c
  • lines changed 2, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/lib/memgfx.c
  • lines changed 1, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/lib/twoBit.c
  • lines changed 6, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/lib/vcf.c
  • lines changed 3, context: html, text, full: html, text
    there is a macro INLINE for static inline refs #12189
• src/makefile
  • lines changed 4, context: html, text, full: html, text
    allow alpha target to work with make -j N parallel make refs #9149
• src/product/scripts/README.trashCleaning
  • lines changed 65, context: html, text, full: html, text
    describe the history of trash cleaning refs #11957
  • lines changed 6, context: html, text, full: html, text
    describe the history of trash cleaning refs #11957
  • lines changed 57, context: html, text, full: html, text
    additional material refs #11957
  • lines changed 22, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
  • lines changed 5, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
  • lines changed 1, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
• src/product/scripts/browserEnvironment.txt
  • lines changed 8, context: html, text, full: html, text
    better defaults for a generic installation refs #11957
• src/product/scripts/cleanLostTables.sh
  • lines changed 54, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
• src/product/scripts/dirStatsFromFind.pl
  • lines changed 228, context: html, text, full: html, text
    generic trash cleaning system now available here refs #11957
• src/product/scripts/fileStatsFromFind.pl
  • lines changed 61, context: html, text, full: html, text
    generic trash cleaning system now available here refs #11957
• src/product/scripts/lostTables.pl
  • lines changed 196, context: html, text, full: html, text
    adding lost table cleaner scripts refs #11957
• src/product/scripts/measureTrash.sh
  • lines changed 70, context: html, text, full: html, text
    generic trash cleaning system now available here refs #11957
• src/product/scripts/trashCleanMonitor.sh
  • lines changed 97, context: html, text, full: html, text
    generic trash cleaning system now available here refs #11957
  • lines changed 6, context: html, text, full: html, text
    now using a bash script for the trash cleaner since minimal Ubuntu systems do not have csh refs #11957
• src/product/scripts/trashCleaner.bash
  • lines changed 381, context: html, text, full: html, text
    now using a bash script for the trash cleaner since minimal Ubuntu systems do not have csh refs #11957
• src/product/scripts/trashCleaner.csh
  • lines changed 87, context: html, text, full: html, text
    now using a bash script for the trash cleaner since minimal Ubuntu systems do not have csh refs #11957
  • lines changed 294, context: html, text, full: html, text
    now using a bash script for the trash cleaner since minimal Ubuntu systems do not have csh refs #11957
• src/product/scripts/trashSizeMonitor.sh
  • lines changed 116, context: html, text, full: html, text
    addition to generic trash cleaner system refs #11957
• src/test/buildTableDescriptions.pl
  • lines changed 1, context: html, text, full: html, text
    avoid the bedToBigBed/tests/input/itemRgb.as duplicate
• src/userApps/fetchKentSource.sh
  • lines changed 6, context: html, text, full: html, text
    improve note about HEAD vs beta branch refs #9149
• src/utils/bedToBigBed/makefile
  • lines changed 4, context: html, text, full: html, text
    do not need the redundant test target refs #9104
• src/utils/bedToBigBed/tests/input/itemRgb.as
  • lines changed 1, context: html, text, full: html, text
    avoid duplicate definition of this structure from src/hg/lib/fullBed.as
  • lines changed 1, context: html, text, full: html, text
    avoid duplicate definition of this structure from src/hg/lib/fullBed.as
• src/utils/faRandomize/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    make sure diff output gets to stderr so we will see the error in email from cron jobs refs #12189
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v293 preview2
• src/utils/qa/weeklybld/buildOneUseCase
  • lines changed 31, context: html, text, full: html, text
    capture scripts from build/bin/scripts refs #12090
• src/utils/qa/weeklybld/buildWithUseCases
  • lines changed 109, context: html, text, full: html, text
    capture scripts from build/bin/scripts refs #12090
• src/utils/qa/weeklybld/runBuildWithUseCases.sh
  • lines changed 2, context: html, text, full: html, text
    capture scripts from build/bin/scripts refs #12090