File Changes for kent

v295_preview to v295_preview2 (2014-01-20 to 2014-01-27) v295

• src/hg/encode3/eap/README
  • lines changed 8, context: html, text, full: html, text
    Adding a paragraph of doc on EAP overall.
• src/hg/encode3/eap/eapAddSoftware/eapAddSoftware.c
  • lines changed 68, context: html, text, full: html, text
    Utility to help make it easier to add new software with version tracking etc now made.
• src/hg/encode3/eap/eapAddSoftware/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to help make it easier to add new software with version tracking etc now made.
• src/hg/encode3/eap/eapAddStep/eapAddStep.c
  • lines changed 230, context: html, text, full: html, text
    Somewhat awkard helper program to add steps to database.
• src/hg/encode3/eap/eapAddStep/makefile
  • lines changed 4, context: html, text, full: html, text
    Somewhat awkard helper program to add steps to database.
• src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c
  • lines changed 215, context: html, text, full: html, text
    Moving one more thing from edw to eap.
  • lines changed 4, context: html, text, full: html, text
    Adapting to new position in source tree.
  • lines changed 6, context: html, text, full: html, text
    Making self references consistent with new self name.
  • lines changed 82, context: html, text, full: html, text
    Adapting to new eapStep schema. Making inputs and outputs arrays.
  • lines changed 2, context: html, text, full: html, text
    Adding a null check
• src/hg/encode3/eap/eapAnalysisJson/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving one more thing from edw to eap.
  • lines changed 2, context: html, text, full: html, text
    Adapting to new position in source tree.
  • lines changed 1, context: html, text, full: html, text
    Adding another library
• src/hg/encode3/eap/eapDaemon/eapDaemon.c
  • lines changed 14, context: html, text, full: html, text
    Adapting to name changes from edw->eap move.
• src/hg/encode3/eap/eapFinish/eapFinish.c
  • lines changed 54, context: html, text, full: html, text
    CHanging many symbols from edwAnalysis... to eap... Adapting to refactoring of eapStep and related tables.
• src/hg/encode3/eap/eapFinish/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding more libraries.
• src/hg/encode3/eap/eapMonitor/eapMonitor.c
  • lines changed 21, context: html, text, full: html, text
    Adding count of waiting jobs to eapMonitor steps command. Making jobs scheduled not include jobs running in status command.
  • lines changed 31, context: html, text, full: html, text
    Improving sorting of eapMonitor steps.
  • lines changed 59, context: html, text, full: html, text
    Added doctor command, which resets counters on all sick batches we own.
  • lines changed 1, context: html, text, full: html, text
    Adding doctor to usage message.
  • lines changed 19, context: html, text, full: html, text
    Renaming edwAnalysis to eap on many symbols. Fixing some corner case crashes.
• src/hg/encode3/eap/eapSchedule/eapSchedule.c
  • lines changed 8, context: html, text, full: html, text
    Adding -step option to limit which steps are taken. Fixing old bug in usage.
  • lines changed 138, context: html, text, full: html, text
    Refactoring for new eapStep and related tables. Killing sneaky up option since now have a separate update utility. Adding inFormat option.
  • lines changed 33, context: html, text, full: html, text
    Changing handling of mixed read length files so eapSchedule warns on them in the hotspot section, and declines to schedule, rather than by aborting with an error message.
• src/hg/encode3/eap/eapSchedule/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding new library.
• src/hg/encode3/eap/eapUpdateSoftware/eapUpdateSoftware.c
  • lines changed 79, context: html, text, full: html, text
    Utility to make it easier to update analysis software and version tables with a new software version seems to work.
• src/hg/encode3/eap/eapUpdateSoftware/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to make it easier to update analysis software and version tables with a new software version seems to work.
• src/hg/encode3/eap/inc/eapDb.h
  • lines changed 713, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 49, context: html, text, full: html, text
    Polishing schema a bit more. First working draft. Still want to rename eapAnalysis table, but it's working for the first time in 48 hours, so time to take a snapshot.
• src/hg/encode3/eap/inc/eapLib.h
  • lines changed 47, context: html, text, full: html, text
    Moving in a bunch of stuff from edwLib, refactoring as needed.
• src/hg/encode3/eap/lib/eapDb.as
  • lines changed 106, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 15, context: html, text, full: html, text
    Polishing schema a bit more. First working draft. Still want to rename eapAnalysis table, but it's working for the first time in 48 hours, so time to take a snapshot.
• src/hg/encode3/eap/lib/eapDb.c
  • lines changed 1776, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 151, context: html, text, full: html, text
    Polishing schema a bit more. First working draft. Still want to rename eapAnalysis table, but it's working for the first time in 48 hours, so time to take a snapshot.
• src/hg/encode3/eap/lib/eapDb.sql
  • lines changed 130, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 19, context: html, text, full: html, text
    Polishing schema a bit more. First working draft. Still want to rename eapAnalysis table, but it's working for the first time in 48 hours, so time to take a snapshot.
• src/hg/encode3/eap/lib/eapLib.c
  • lines changed 229, context: html, text, full: html, text
    Moving in a bunch of stuff from edwLib, refactoring as needed.
  • lines changed 12, context: html, text, full: html, text
    Adapting to schema changes in edw->eap transition.
• src/hg/encode3/eap/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving some of encodeDataWarehouse.as output to eapDb.as
• src/hg/encode3/eap/lib/redoSchema
  • lines changed 4, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 1, context: html, text, full: html, text
    Making resetDb properly build up software and step tables.
• src/hg/encode3/eap/lib/resetDb
  • lines changed 8, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 34, context: html, text, full: html, text
    Making resetDb properly build up software and step tables.
• src/hg/encode3/eap/makefile
  • lines changed 9, context: html, text, full: html, text
    Fixed typo, added eapAnalysisJson, and fixed it so high level make builds everything instead of just lib
• src/hg/encode3/encodeDataWarehouse/edwAddAssembly/edwAddAssembly.c
  • lines changed 6, context: html, text, full: html, text
    Including seqCount in edwAssembly
• src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c
  • lines changed 215, context: html, text, full: html, text
    Moving one more thing from edw to eap.
• src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving one more thing from edw to eap.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/sorted.bed
  • lines changed 331449, context: html, text, full: html, text
    Didn't mean to commit this, oops.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 19, context: html, text, full: html, text
    Moving a bunch of stuff from edwLib to eapLib.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 290, context: html, text, full: html, text
    Moving a bunch of stuff from edw tables to eap ones, reformatting tables a bit in the process.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 99, context: html, text, full: html, text
    Moving a bunch of stuff from edwLib to eapLib.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 58, context: html, text, full: html, text
    Moving a bunch of stuff from edw tables to eap ones, reformatting tables a bit in the process.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 928, context: html, text, full: html, text
    Moving a bunch of stuff from edw tables to eap ones, reformatting tables a bit in the process.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 67, context: html, text, full: html, text
    Moving a bunch of stuff from edw tables to eap ones, reformatting tables a bit in the process.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 37, context: html, text, full: html, text
    Adding admin privs to some users, X and Y chroms to enrichment targets, resyncing with Stanford.
• src/hg/encode3/encodeDataWarehouse/lib/restartDaemons
  • lines changed 2, context: html, text, full: html, text
    Taking out analysis daemon. Wanting to start that separately.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving edwAnalysisAddJob to eap side of the world.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c
  • lines changed 2, context: html, text, full: html, text
    Adding in a NULL check on response from Stanford
• src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwToEap1.c
  • lines changed 386, context: html, text, full: html, text
    Tool to convert analysis tables from edw to eap format seems to work.
  • lines changed 1, context: html, text, full: html, text
    Oops, forgot return code!
• src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/makefile
  • lines changed 4, context: html, text, full: html, text
    Tool to convert analysis tables from edw to eap format seems to work.
• src/hg/inc/jksql.h
  • lines changed 4, context: html, text, full: html, text
    Exporting sqlExcapeTabFileString and improving it's opening comment.
• src/hg/lib/jksql.c
  • lines changed 2, context: html, text, full: html, text
    Exporting sqlExcapeTabFileString and improving it's opening comment.
• src/hg/oneShot/freen/freen.c
  • lines changed 9, context: html, text, full: html, text
    Freen tests ways to parse comma separated lists
• src/hg/utils/gffToBed/test.gff
  • lines changed 61300, context: html, text, full: html, text
    Getting rid of a test input that is too big.
• src/inc/common.h
  • lines changed 10, context: html, text, full: html, text
    Adding slUnsigned to our basic listy types like slInt...
• src/lib/bbiWrite.c
  • lines changed 10, context: html, text, full: html, text
    Improving handling of empty data sets by bedToBigBed and bigBedInfo.
• src/lib/cirTree.c
  • lines changed 7, context: html, text, full: html, text
    Improving handling of empty data sets by bedToBigBed and bigBedInfo.
• src/lib/common.c
  • lines changed 9, context: html, text, full: html, text
    Adding slUnsigned to our basic listy types like slInt...
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    Expanded libraries that get tagged.
• src/parasol/inc/paraVersion.h
  • lines changed 1, context: html, text, full: html, text
    Documenting code change and bumping version.
• src/parasol/parasol/parasol.c
  • lines changed 2, context: html, text, full: html, text
    Fixing command line usage statement problem Galt fingered in review.
• src/parasol/version.doc
  • lines changed 2, context: html, text, full: html, text
    Documenting code change and bumping version.
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 13, context: html, text, full: html, text
    Improving handling of empty data sets by bedToBigBed and bigBedInfo.
  • lines changed 4, context: html, text, full: html, text
    Bumped version number and started version log.
• src/utils/bigBedInfo/bigBedInfo.c
  • lines changed 8, context: html, text, full: html, text
    Improving handling of empty data sets by bedToBigBed and bigBedInfo.