Commits for kent

v301_preview2 to v301_base (2014-06-02 to 2014-06-09) v301

• Upgraded command line so can select from one of three graph types and also several options.
  • src/hg/oneShot/tryGtexBoxPlot/tryGtexBoxPlot.c - lines changed 188, context: html, text, full: html, text
• Restricting scheduling to output of previous step for now.
  • src/hg/encode3/eap/eapSchedule/eapSchedule.c - lines changed 25, context: html, text, full: html, text
• Bumping version to 2.
  • src/hg/encode3/encodeDataWarehouse/utils/edwBamFilter/edwBamFilter.c - lines changed 2, context: html, text, full: html, text
• Looking for NULL as well as 'null'
  • src/hg/lib/hgExp.c - lines changed 1, context: html, text, full: html, text
• Added encode3BedType structure and a table of these so that there is hopefully just one place where we store info about the as files we accept for ENCODE.
  • src/hg/inc/encode3/encode3Valid.h - lines changed 17, context: html, text, full: html, text
  • src/hg/lib/encode3/encode3Valid.c - lines changed 34, context: html, text, full: html, text
• Changing to use encode3BedType library shared by warehouse and validators.
  • src/hg/encode3/validateManifest/validateManifest.c - lines changed 61, context: html, text, full: html, text
• Adding support for bed_ formats to warehouse.
  • src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c - lines changed 55, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 59, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 22, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 15, context: html, text, full: html, text
• Dealing with changes in Stanford URLs. Making biosample getter cache
  • src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c - lines changed 44, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c - lines changed 4, context: html, text, full: html, text