Commits for kent

v287_preview2 to v287_base (2013-07-23 to 2013-07-30) v287

• First cut seems to work.
  • src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c - lines changed 163, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/makefile - lines changed 16, context: html, text, full: html, text
• Adding support for replacement operations.
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 112, context: html, text, full: html, text
• Adding little script to send it to San Diego.
  • src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/makk - lines changed 3, context: html, text, full: html, text
• Making new edwCorrectFileTags utility to correct file tags after upload. Moving stuff from edwChangeFormat to library to reuse in this context.
  • src/hg/encode3/encodeDataWarehouse/edwChangeFormat/edwChangeFormat.c - lines changed 47, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/edwCorrectFileTags.c - lines changed 104, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/makk - lines changed 3, 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 31, context: html, text, full: html, text
  • src/inc/cheapcgi.h - lines changed 5, context: html, text, full: html, text
  • src/lib/cheapcgi.c - lines changed 26, context: html, text, full: html, text
• Improving memory management.
  • src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c - lines changed 3, context: html, text, full: html, text
• Improving comment.
  • src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c - lines changed 1, context: html, text, full: html, text
• Whitelisting Cricket under her Stanford email.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 2, context: html, text, full: html, text
• Seems to work.
  • src/hg/encode3/encodeDataWarehouse/edwAddQaContamTarget/edwAddQaContamTarget.c - lines changed 52, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwAddQaContamTarget/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwAddQaContamTarget/makk - lines changed 3, context: html, text, full: html, text
• Adding functions to sum up size of all ranges in tree.
  • src/inc/genomeRangeTree.h - lines changed 2, context: html, text, full: html, text
  • src/lib/genomeRangeTree.c - lines changed 11, context: html, text, full: html, text
  • src/lib/rangeTree.c - lines changed 18, context: html, text, full: html, text
• Defining tables for contamination screening.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 152, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 17, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 355, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 21, context: html, text, full: html, text
• Moving edwAlignFastqMakeBed from edwMakeValid file to library so it can be shared.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 5, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 87, context: html, text, full: html, text
• Moving several routines to library. Supporting fasta files.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 133, context: html, text, full: html, text
• Adding fasta files.
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 1, context: html, text, full: html, text
• Changing connect to use librrary routine.
  • src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c - lines changed 1, context: html, text, full: html, text
• Adding a bunch of assemblies for use as contamination targets. Adding Katrina and Chin to white list.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 12, context: html, text, full: html, text
• Adding functions to sum up size of all ranges in tree.
  • src/inc/rangeTree.h - lines changed 7, context: html, text, full: html, text
• Added several new edw programs to higher level make.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 4, context: html, text, full: html, text