All File Changes

v310_preview to v310_preview2 (2014-12-08 to 2014-12-15) v310

• src/beacon/README.txt
  • lines changed 36, context: html, text, full: html, text
    largely revamped beacon, refs #14393
• src/beacon/accCounts.gdbm
  • lines changed 0, context: html, text, full: html, text
    largely revamped beacon, refs #14393
• src/beacon/insdcToUcsc.tab
  • lines changed 93, context: html, text, full: html, text
    largely revamped beacon, refs #14393
• src/beacon/makefile
  • lines changed 53, context: html, text, full: html, text
    largely revamped beacon, refs #14393
• src/beacon/query
  • lines changed 156, context: html, text, full: html, text
    largely revamped beacon, refs #14393
• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    Bumped version number.
• src/browserbox/root/updateBrowser.sh
  • lines changed 19, context: html, text, full: html, text
    changes after code review refs #14501
• src/hg/cirm/cdw/cdwAddAssembly/cdwAddAssembly.c
  • lines changed 89, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
  • lines changed 1, context: html, text, full: html, text
    Getting to compile again after moving a .h file.
• src/hg/cirm/cdw/cdwAddAssembly/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwAddQaContamTarget/cdwAddQaContamTarget.c
  • lines changed 55, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwAddQaContamTarget/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwAddQaEnrichTarget/cdwAddQaEnrichTarget.c
  • lines changed 91, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
  • lines changed 1, context: html, text, full: html, text
    Getting to compile again after moving a .h file.
• src/hg/cirm/cdw/cdwAddQaEnrichTarget/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwAddSubscriber/cdwAddSubscriber.c
  • lines changed 93, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwAddSubscriber/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwChangeFormat/cdwChangeFormat.c
  • lines changed 83, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwChangeFormat/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwCorrectFileTags/cdwCorrectFileTags.c
  • lines changed 143, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwCorrectFileTags/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwCreateUser/cdwCreateUser.c
  • lines changed 44, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwCreateUser/makefile
  • lines changed 19, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwFakeManifestFromSubmit/cdwFakeManifestFromSubmit.c
  • lines changed 132, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwFakeManifestFromSubmit/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwJob/cdwJob.c
  • lines changed 159, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwJob/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeContaminationQa/cdwMakeContaminationQa.c
  • lines changed 198, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeContaminationQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c
  • lines changed 541, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeEnrichments/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c
  • lines changed 306, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakePairedEndQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeRepeatQa/cdwMakeRepeatQa.c
  • lines changed 127, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeRepeatQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeReplicateQa/cdwMakeReplicateQa.c
  • lines changed 525, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeReplicateQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 730, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
  • lines changed 1, context: html, text, full: html, text
    Getting to compile again after moving a .h file.
• src/hg/cirm/cdw/cdwMakeValidFile/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeWigSpotQa/cdwMakeWigSpotQa.c
  • lines changed 124, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwMakeWigSpotQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwQaEvaluate/cdwQaEvaluate.c
  • lines changed 577, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwQaEvaluate/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwReallyRemoveFiles/cdwReallyRemoveFiles.c
  • lines changed 142, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwReallyRemoveFiles/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwRetryJob/cdwRetryJob.c
  • lines changed 100, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwRetryJob/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwRunDaemon/cdwRunDaemon.c
  • lines changed 336, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwRunDaemon/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwRunOnIds/cdwRunOnIds.c
  • lines changed 62, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwRunOnIds/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 1171, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwSubmit/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwUndeprecate/cdwUndeprecate.c
  • lines changed 57, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwUndeprecate/makefile
  • lines changed 4, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebAuthLogin/cdwWebAuthLogin.c
  • lines changed 110, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebAuthLogin/makefile
  • lines changed 16, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebAuthLogout/cdwWebAuthLogout.c
  • lines changed 18, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebAuthLogout/makefile
  • lines changed 16, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 486, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebBrowse/makefile
  • lines changed 16, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebCreateUser/cdwWebCreateUser.c
  • lines changed 72, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebCreateUser/makefile
  • lines changed 16, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebDeprecate/cdwWebDeprecate.c
  • lines changed 209, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebDeprecate/makefile
  • lines changed 16, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebSubmit/cdwWebSubmit.c
  • lines changed 352, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/cdwWebSubmit/makefile
  • lines changed 16, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 2013, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/inc/cdwBamFileFromRa.h
  • lines changed 18, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/inc/cdwFastqFileFromRa.h
  • lines changed 18, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 369, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/inc/cdwQaWigSpotFromRa.h
  • lines changed 21, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/inc/cdwValid.h
  • lines changed 42, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 387, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 5145, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 458, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/lib/cdwBamFileFromRa.c
  • lines changed 210, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/lib/cdwFastqFileFromRa.c
  • lines changed 309, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 1693, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/lib/cdwQaWigSpotFromRa.c
  • lines changed 139, context: html, text, full: html, text
    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/lib/cdwValid.c
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    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/lib/makefile
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    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/cdw/makefile
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    Initial import of encodeDataWarehouse code base to make CIRM data warehouse. Mostly this is just automatic string substitutions of 'cdw' for 'edw', 'CIRM' for 'ENCODE', and so forth. Also got rid of a lot of programs that won't be relevant.
• src/hg/cirm/quakeLab/djangoModelToAs/djangoModelToAs.c
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    Adding auto-id, and handling text fields.
• src/hg/hgBeacon/README.txt
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    largely revamped beacon, refs #14393
• src/hg/hgBeacon/hgBeacon
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    largely revamped beacon, refs #14393
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    small formatting changes in last commit
• src/hg/hgBeacon/makefile
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    largely revamped beacon, refs #14393
• src/hg/hgTracks/bedTrack.c
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    new tdb statement "labelOnFeature", refs #14512
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    adding a linkIdInName tdb statement, refs #14534
• src/hg/hgTracks/hgTracks.h
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    new tdb statement "labelOnFeature", refs #14512
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    changes in response to code review #14504
• src/hg/hgTracks/simpleTracks.c
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    Simplifying pack visibility logic for clickmaps and next/prev exon arrows.
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    new tdb statement "labelOnFeature", refs #14512
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    changes in response to code review #14504
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    adding a linkIdInName tdb statement, refs #14534
• src/hg/htdocs/FAQ/FAQreleases.html
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    Editing docs for dm6 release, refs #4049
• src/hg/htdocs/goldenPath/credits.html
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    Editing docs for dm6 release, refs #4049
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
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    tdb doc for labelOnFeature, refs #14512
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
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    tdb doc for labelOnFeature, refs #14512
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    tdb doc for labelOnFeature, refs #14512
• src/hg/htdocs/goldenPath/newsarch.html
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    Adding announcement for dm6 release, refd #40449
• src/hg/htdocs/images/genomeMan200.jpg
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• src/hg/htdocs/images/training/vidTitle02.jpg
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• src/hg/htdocs/images/training/vidTitle03.jpg
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    Adding training video title images. refs #13854 #13822 #13855
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• src/hg/htdocs/images/training/vidTitle04.jpg
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    Adding training video title images. refs #13854 #13822 #13855
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    made video icons files smaller
• src/hg/htdocs/indexNews.html
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    Adding announcement for dm6 release, refd #40449
• src/hg/htdocs/makefile
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    Adding some helpful reminder comments to htdocs makefile about rsyncing files which have not been checked in yet.
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    adding ashg2014 content to training pages
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    adding ashg2014 content to training pages
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    adding ashg2014 content to training pages
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    adding ashg2014 content to training pages
• src/hg/htdocs/training/ashg2014/genelist
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    adding ashg2014 content to training pages
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    adding ashg2014 content to training pages
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• src/hg/htdocs/training/ashg2014/remoteDataExamples.html
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    adding ashg2014 content to training pages
• src/hg/htdocs/training/index.html
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    adding ashg2014 content to training pages
• src/hg/htdocs/training/vids/vid01.html
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    Adding in individual page for first training video. refs #13853
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    made browser open a new window when launching transcript01.pdf
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    Adding topbar to vid page. refs #13853
• src/hg/htdocs/training/vids/vid02.html
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    Adding individual pages for other training videos. refs #13854 #13822 #13855
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    Adding top bar code to training vid pages. refs #14525
• src/hg/htdocs/training/vids/vid03.html
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    Adding individual pages for other training videos. refs #13854 #13822 #13855
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    Adding top bar code to training vid pages. refs #14525
• src/hg/htdocs/training/vids/vid04.html
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    Adding individual pages for other training videos. refs #13854 #13822 #13855
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    Adding top bar code to training vid pages. refs #14525
• src/hg/js/hgTracks.js
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    Fixes 14509. hgTracks.js had an incorrect assumption that the position to be updated in the document title would always be in the 2nd position after parsing on spaces. But "D. melanogaster" and several others which used the scientific name would break. It was tricky because it could get fixed by certain refreshes. The new hgTracks.js needs to get pushed with this release. The fix involves simply scanning for a word that contains a colon character which should only appear in the position field, and does not appear in dbDb names or sci-names.
• src/hg/lib/hui.c
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    changes in response to code review #14504
• src/hg/makeDb/doc/anoGam1.txt
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    add procedure for swap dm6 chain net refs #4049
• src/hg/makeDb/doc/bosTau8.txt
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    lastz to equCab2 done correctly refs #14221
• src/hg/makeDb/doc/droPer1.txt
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    add procedure for swap dm6 chain net refs #4049
• src/hg/makeDb/doc/droSec1.txt
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    add procedure for swap dm6 chain net refs #4049
• src/hg/makeDb/doc/droSim1.txt
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    add procedure for swap dm6 chain net refs #4049
• src/hg/makeDb/doc/eboVir3/iedbPred.txt
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    forgot makedoc for iedbPred ebola track, refs #14467
• src/hg/makeDb/doc/encode3/hg38_encode2_dnase1.txt
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    Improved comments
• src/hg/makeDb/doc/felCat5.txt
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    liftOver to felCat8 refs #14412
• src/hg/makeDb/doc/felCat8/initialBuild.txt
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    build is almost ready to push refs #14412
• src/hg/makeDb/doc/felCat8/ucscCompositeAgp.pl
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    build is almost ready to push refs #14412
• src/hg/makeDb/doc/felCat8/ucscToINSDC.sh
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    build is almost ready to push refs #14412
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    build is almost ready to push refs #14412
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    build is almost ready to push refs #14412
• src/hg/makeDb/doc/hg19.txt
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    Added VCF track for ExAC (Exome Aggregation Consortium) variants. There is also a file of targeted regions; I'm considering adding that and making a composite of variants + regions. refs #14379
• src/hg/makeDb/doc/hg38/hg38.txt
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    Prep for new track build
• src/hg/makeDb/doc/makeEnsembl.txt
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    v78 update complete refs #14462
• src/hg/makeDb/doc/mm10.txt
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    import GENCODE mouse VM4
• src/hg/makeDb/doc/tarSyr2/initialBuild.txt
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    done through genbank runs refs #14410
• src/hg/makeDb/genbank/etc/align.dbs
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    Added tarSyr2 - Tarsier refs #14410
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    Adding dm6 to hgwbeta genbank updates, refs #4049
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    Added tarSyr2 - Tarsier refs #14410
• src/hg/makeDb/genbank/etc/rr.dbs
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    Adding dm6 to RR GenBank updates, refs #4049
• src/hg/makeDb/schema/all.joiner
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    import GENCODE mouse VM4
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbPred.html
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    fixing broken links and overall org of iedbPred ebola tracks, refs #14467
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    removing ref, refs #14467
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    Corrections to eboVir3 iedbPred track desc pages, refs #14467
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbPred1.html
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    fixing broken links and overall org of iedbPred ebola tracks, refs #14467
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    removing ref, refs #14467
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    Corrections to eboVir3 iedbPred track desc pages, refs #14467
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbPredClassIMac.html
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    fixing broken links and overall org of iedbPred ebola tracks, refs #14467
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    removing ref, refs #14467
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    Corrections to eboVir3 iedbPred track desc pages, refs #14467
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbSupp3.html
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    fixing broken links and overall org of iedbPred ebola tracks, refs #14467
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    Corrections to eboVir3 iedbPred track desc pages, refs #14467
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.iedbPred.ra
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    fixing broken links and overall org of iedbPred ebola tracks, refs #14467
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.iedbPred1.ra
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    fixing broken links and overall org of iedbPred ebola tracks, refs #14467
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.iedbPred2.ra
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    fixing broken links and overall org of iedbPred ebola tracks, refs #14467
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
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    again trying to fix the uniprot track visibility on ebola
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    removed two superfluous lines in last commit
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    fixing broken links and overall org of iedbPred ebola tracks, refs #14467
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    catching up with primate chain net packaging refs #10272
• src/hg/makeDb/trackDb/human/chainNetStray.ra
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    catching up with primate chain net packaging refs #10272
• src/hg/makeDb/trackDb/human/chainNetTarSyr1.ra
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    catching up with primate packaging refs #14410
• src/hg/makeDb/trackDb/human/chainNetTarSyr2.ra
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    catching up with primate packaging refs #14410
• src/hg/makeDb/trackDb/human/hg19/exacVariants.html
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    Added VCF track for ExAC (Exome Aggregation Consortium) variants. There is also a file of targeted regions; I'm considering adding that and making a composite of variants + regions. refs #14379
• src/hg/makeDb/trackDb/human/hg19/haibTfbs.txt
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    Remove temp files
• src/hg/makeDb/trackDb/human/hg19/tfbsRanges.txt
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    Remove temp files
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    new tdb statement "labelOnFeature", refs #14512
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    Added VCF track for ExAC (Exome Aggregation Consortium) variants. There is also a file of targeted regions; I'm considering adding that and making a composite of variants + regions. refs #14379
• src/hg/makeDb/trackDb/human/hg19/viewLimits.txt
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    Remove temp files
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    import GENCODE mouse VM4
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
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    import GENCODE mouse VM4
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM4.html
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    import GENCODE mouse VM4
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM4.ra
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    import GENCODE mouse VM4
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    Adding new lastz reference to a few missed assemblies, refs #14061
• src/hg/makeDb/trackDb/proboscis/nasLar1/gap.html
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    update with better gap definitions refs #14437
• src/hg/makeDb/trackDb/proboscis/nasLar1/gold.html
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    update with better gap definitions refs #14437
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
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    Adding new lastz reference to a few missed assemblies, refs #14061
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
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    Adding new lastz reference to a few missed assemblies, refs #14061
• src/hg/makeDb/trackDb/tagTypes.tab
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    new tdb statement "labelOnFeature", refs #14512
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    adding a linkIdInName tdb statement, refs #14534
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
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    adding chlSab2 refs #11172
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    adding papAnu2 otoGar3 and nomLeu3 refs #14439
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    adding tarSyr2 refs #14410
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    adding papAnu2 otoGar3 and nomLeu3 refs #14439
• src/hg/makeDb/trackDb/trackDb.ra
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    import GENCODE mouse VM4
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
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    Adding new lastz reference to a few missed assemblies, refs #14061
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
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    Adding new lastz reference to a few missed assemblies, refs #14061
• src/hg/utils/automation/makeGenomeDb.pl
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    need to have trackDb.chainNet.insects.ra for trackDb build refs #14437
• src/inc/genoFind.h
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    Bumping version

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