Commits for hiram

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

• bringing genscan up to date on all 100-way involved species refs #10272
  • src/hg/makeDb/doc/ailMel1.txt - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/doc/anoCar2.txt - lines changed 113, context: html, text, full: html, text
  • src/hg/makeDb/doc/calJac3.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/danRer7.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/equCab2.txt - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/falPer1.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/gasAcu1.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/loxAfr3.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/macEug2.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/melGal1.txt - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/doc/myoLuc2.txt - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/oryCun2.txt - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/doc/oryLat2.txt - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/doc/tetNig2.txt - lines changed 22, context: html, text, full: html, text
• complete ensGene lift from taeGut1 with all ens tables refs #10272
  • src/hg/makeDb/doc/taeGut2.txt - lines changed 23, context: html, text, full: html, text
• do not need the redundant test target refs #9104
  • src/utils/bedToBigBed/makefile - lines changed 4, context: html, text, full: html, text
• avoid duplicate definition of this structure from src/hg/lib/fullBed.as
  • src/utils/bedToBigBed/tests/input/itemRgb.as - lines changed 1, context: html, text, full: html, text
• allow alpha target to work with make -j N parallel make refs #9149
  • src/makefile - lines changed 4, context: html, text, full: html, text
• capture scripts from build/bin/scripts refs #12090
  • src/utils/qa/weeklybld/buildOneUseCase - lines changed 31, context: html, text, full: html, text
  • src/utils/qa/weeklybld/buildWithUseCases - lines changed 109, context: html, text, full: html, text
  • src/utils/qa/weeklybld/runBuildWithUseCases.sh - lines changed 2, context: html, text, full: html, text
• temporary disable USE_HAL check to verify refs #12119
  • src/hg/hgTables/hal.c - lines changed 7, context: html, text, full: html, text
• remove temporary disable USE_HAL check to verify refs #12119
  • src/hg/hgTables/hal.c - lines changed 7, 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/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/hg/liftOver/tests/makefile - lines changed 16, context: html, text, full: html, text
• there is a macro INLINE for static inline refs #12189
  • src/lib/cirTree.c - lines changed 2, context: html, text, full: html, text
  • src/lib/elmTree.c - lines changed 2, context: html, text, full: html, text
  • src/lib/memgfx.c - lines changed 1, context: html, text, full: html, text
  • src/lib/twoBit.c - lines changed 6, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 3, context: html, text, full: html, text
• remove redundant set of parens refs #12209
  • src/lib/common.c - lines changed 1, context: html, text, full: html, text
• remove redundant semi-colon refs #12209
  • src/hg/lib/jsHelper.c - lines changed 1, context: html, text, full: html, text
• make sure numChanged and numMatched are initialzed properly before use refs #12209
  • src/hg/lib/jksql.c - lines changed 2, context: html, text, full: html, text
• fix broken if statement refs #12209
  • src/hg/lib/hgMaf.c - lines changed 1, context: html, text, full: html, text
• correctly initialize sizeOne before use refs @12209
  • src/hg/lib/imageClone.c - lines changed 1, context: html, text, full: html, text
• improve note about HEAD vs beta branch refs #9149
  • src/userApps/fetchKentSource.sh - lines changed 6, context: html, text, full: html, text
• correctly size 8 byte array for swapping routines refs @12209
  • src/lib/common.c - 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/doCpgIslands.pl - lines changed 2, context: html, text, full: html, text
• generic trash cleaning system now available here refs #11957
  • src/product/scripts/dirStatsFromFind.pl - lines changed 228, context: html, text, full: html, text
  • src/product/scripts/fileStatsFromFind.pl - lines changed 61, context: html, text, full: html, text
  • src/product/scripts/measureTrash.sh - lines changed 70, context: html, text, full: html, text
  • src/product/scripts/trashCleanMonitor.sh - lines changed 97, 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/trashCleanMonitor.sh - lines changed 6, context: html, text, full: html, text
  • 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
  • src/product/scripts/trashCleaner.csh - lines changed 294, context: html, text, full: html, text
• better defaults for a generic installation refs #11957
  • src/product/scripts/browserEnvironment.txt - lines changed 8, context: html, text, full: html, text
• addition to generic trash cleaner system refs #11957
  • src/product/scripts/trashSizeMonitor.sh - lines changed 116, context: html, text, full: html, text
• describe the history of trash cleaning refs #11957
  • src/product/scripts/README.trashCleaning - lines changed 65, context: html, text, full: html, text
• describe the history of trash cleaning refs #11957
  • src/product/scripts/README.trashCleaning - lines changed 6, context: html, text, full: html, text
• additional material refs #11957
  • src/product/scripts/README.trashCleaning - lines changed 57, 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/dbCommonScientificCladeOrderkey.tab - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/placentals.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 3, context: html, text, full: html, text
• adding lost table cleaner scripts refs #11957
  • src/product/scripts/cleanLostTables.sh - lines changed 54, context: html, text, full: html, text
  • src/product/scripts/lostTables.pl - lines changed 196, context: html, text, full: html, text
• adding lost table cleaner scripts refs #11957
  • src/product/scripts/README.trashCleaning - lines changed 22, context: html, text, full: html, text
• adding lost table cleaner scripts refs #11957
  • src/product/scripts/README.trashCleaning - lines changed 5, context: html, text, full: html, text
• adding lost table cleaner scripts refs #11957
  • src/product/scripts/README.trashCleaning - lines changed 1, context: html, text, full: html, text
• avoid duplicate definition of this structure from src/hg/lib/fullBed.as
  • src/utils/bedToBigBed/tests/input/itemRgb.as - lines changed 1, 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/HgRemoteScript.pm - lines changed 39, context: html, text, full: html, text
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 55, context: html, text, full: html, text
• avoid the bedToBigBed/tests/input/itemRgb.as duplicate
  • src/test/buildTableDescriptions.pl - lines changed 1, context: html, text, full: html, text
• prepare bigBed files for assembly hub refs #11681
  • src/hg/utils/automation/doGenscan.pl - lines changed 8, context: html, text, full: html, text
• adding apiMel4 Honey bee for assembly hub build refs #11681
  • src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab - lines changed 1, context: html, text, full: html, text
• construct bigBed files for repeat masker result refs #11681
  • 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/utils/automation/rmskBed6+10.pl - lines changed 34, context: html, text, full: html, text
• catching up config files refs #10272
  • src/hg/utils/automation/configFiles/allMis1.config.ra - lines changed 23, context: html, text, full: html, text
  • src/hg/utils/automation/configFiles/papHam1.config.ra - lines changed 24, context: html, text, full: html, text
• v293 preview2
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text