Commits for kent

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

• Improving handling of empty data sets by bedToBigBed and bigBedInfo.
  • src/lib/bbiWrite.c - lines changed 10, context: html, text, full: html, text
  • src/lib/cirTree.c - lines changed 7, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c - lines changed 13, context: html, text, full: html, text
  • src/utils/bigBedInfo/bigBedInfo.c - lines changed 8, context: html, text, full: html, text
• Bumped version number and started version log.
  • src/utils/bedToBigBed/bedToBigBed.c - lines changed 4, 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.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 21, context: html, text, full: html, text
• Improving sorting of eapMonitor steps.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 31, context: html, text, full: html, text
• Fixing command line usage statement problem Galt fingered in review.
  • src/parasol/parasol/parasol.c - lines changed 2, context: html, text, full: html, text
• Documenting code change and bumping version.
  • src/parasol/inc/paraVersion.h - lines changed 1, context: html, text, full: html, text
  • src/parasol/version.doc - lines changed 2, context: html, text, full: html, text
• Adding a paragraph of doc on EAP overall.
  • src/hg/encode3/eap/README - lines changed 8, context: html, text, full: html, text
• Adding -step option to limit which steps are taken. Fixing old bug in usage.
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - 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.
  • src/hg/encode3/eap/inc/eapDb.h - lines changed 713, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.as - lines changed 106, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.c - lines changed 1776, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.sql - lines changed 130, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/redoSchema - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/resetDb - lines changed 8, context: html, text, full: html, text
• Didn't mean to commit this, oops.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/sorted.bed - lines changed 331449, context: html, text, full: html, text
• Added doctor command, which resets counters on all sick batches we own.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 59, context: html, text, full: html, text
• Adding doctor to usage message.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 1, context: html, text, full: html, text
• Tool to convert analysis tables from edw to eap format seems to work.
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwToEap1.c - lines changed 386, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/makefile - lines changed 4, context: html, text, full: html, text
• Moving one more thing from edw to eap.
  • src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c - lines changed 215, context: html, text, full: html, text
  • src/hg/encode3/eap/eapAnalysisJson/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c - lines changed 215, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/makefile - lines changed 4, context: html, text, full: html, text
• Adapting to new position in source tree.
  • src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/eap/eapAnalysisJson/makefile - lines changed 2, context: html, text, full: html, text
• Making self references consistent with new self name.
  • src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c - lines changed 6, 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/eap/makefile - lines changed 9, context: html, text, full: html, text
• Adapting to name changes from edw->eap move.
  • src/hg/encode3/eap/eapDaemon/eapDaemon.c - lines changed 14, context: html, text, full: html, text
• Getting rid of a test input that is too big.
  • src/hg/utils/gffToBed/test.gff - lines changed 61300, 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/eapAddSoftware.c - lines changed 68, context: html, text, full: html, text
  • src/hg/encode3/eap/eapAddSoftware/makefile - lines changed 4, context: html, text, full: html, text
• Somewhat awkard helper program to add steps to database.
  • src/hg/encode3/eap/eapAddStep/eapAddStep.c - lines changed 230, context: html, text, full: html, text
  • src/hg/encode3/eap/eapAddStep/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/eapUpdateSoftware/eapUpdateSoftware.c - lines changed 79, context: html, text, full: html, text
  • src/hg/encode3/eap/eapUpdateSoftware/makefile - lines changed 4, context: html, text, full: html, text
• Expanded libraries that get tagged.
  • src/makefile - lines changed 1, context: html, text, full: html, text
• Adding slUnsigned to our basic listy types like slInt...
  • src/inc/common.h - lines changed 10, context: html, text, full: html, text
  • src/lib/common.c - lines changed 9, context: html, text, full: html, text
• Freen tests ways to parse comma separated lists
  • src/hg/oneShot/freen/freen.c - lines changed 9, context: html, text, full: html, text
• Exporting sqlExcapeTabFileString and improving it's opening comment.
  • src/hg/inc/jksql.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/jksql.c - lines changed 2, 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/inc/encodeDataWarehouse.h - lines changed 290, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 58, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 928, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 67, context: html, text, full: html, text
• Moving a bunch of stuff from edwLib to eapLib.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 19, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 99, context: html, text, full: html, text
• Taking out analysis daemon. Wanting to start that separately.
  • src/hg/encode3/encodeDataWarehouse/lib/restartDaemons - lines changed 2, 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/resetEdw - lines changed 37, context: html, text, full: html, text
• Adding in a NULL check on response from Stanford
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c - lines changed 2, context: html, text, full: html, text
• Oops, forgot return code!
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwToEap1.c - lines changed 1, context: html, text, full: html, text
• Moving edwAnalysisAddJob to eap side of the world.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 1, context: html, text, full: html, text
• Including seqCount in edwAssembly
  • src/hg/encode3/encodeDataWarehouse/edwAddAssembly/edwAddAssembly.c - lines changed 6, 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/eapDb.h - lines changed 49, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.as - lines changed 15, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.c - lines changed 151, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapDb.sql - lines changed 19, context: html, text, full: html, text
• Moving in a bunch of stuff from edwLib, refactoring as needed.
  • src/hg/encode3/eap/inc/eapLib.h - lines changed 47, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/eapLib.c - lines changed 229, context: html, text, full: html, text
• Moving some of encodeDataWarehouse.as output to eapDb.as
  • src/hg/encode3/eap/lib/makefile - lines changed 1, context: html, text, full: html, text
• Making resetDb properly build up software and step tables.
  • src/hg/encode3/eap/lib/redoSchema - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/eap/lib/resetDb - lines changed 34, context: html, text, full: html, text
• Renaming edwAnalysis to eap on many symbols. Fixing some corner case crashes.
  • src/hg/encode3/eap/eapMonitor/eapMonitor.c - lines changed 19, 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.
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 138, context: html, text, full: html, text
• Adding more libraries.
  • src/hg/encode3/eap/eapFinish/makefile - lines changed 1, 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/eapFinish.c - lines changed 54, context: html, text, full: html, text
• Adding new library.
  • src/hg/encode3/eap/eapSchedule/makefile - lines changed 1, context: html, text, full: html, text
• Adapting to new eapStep schema. Making inputs and outputs arrays.
  • src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c - lines changed 82, context: html, text, full: html, text
• Adding another library
  • src/hg/encode3/eap/eapAnalysisJson/makefile - lines changed 1, context: html, text, full: html, text
• Adding a null check
  • src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c - lines changed 2, context: html, text, full: html, text
• Adapting to schema changes in edw->eap transition.
  • src/hg/encode3/eap/lib/eapLib.c - lines changed 12, 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/eapSchedule.c - lines changed 33, context: html, text, full: html, text
• Resolving merge conflict on usage message. Galt's wording was better so kept it.