Commits for tdreszer

v279_preview2 to v279_base (2013-02-05 to 2013-02-12) v279

• Dropped lmFlushZ function at Angie's request. It added little value over lmCleanup/lmInit.
  • src/inc/localmem.h - lines changed 4, context: html, text, full: html, text
  • src/lib/localmem.c - lines changed 12, context: html, text, full: html, text
• Added slSortMerge and slSortMergeUniq at Angie's request. These functions are little more than wrappers for slSort and slUniqify but are still valuable additions.
  • src/lib/common.c - lines changed 18, context: html, text, full: html, text
• Some changes requested by Angie in code review, along with a bug fix. Next checkin will break out the vcfBits routines into separate .c/.h files
  • src/inc/vcf.h - lines changed 14, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 59, context: html, text, full: html, text
• Should have been checked in with common.c. Added slSortMerge and slSortMergeUniq at Angie's request.
  • src/inc/common.h - lines changed 8, context: html, text, full: html, text
• Name changes to clarify code, made at Angie's request. No functional changes here.
  • src/lib/elmTree.c - lines changed 39, context: html, text, full: html, text
• Split vcfBits.c/.h off from vcf.c/.h. No code changes made.
  • src/inc/vcf.h - lines changed 110, context: html, text, full: html, text
  • src/inc/vcfBits.h - lines changed 120, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 450, context: html, text, full: html, text
  • src/lib/vcfBits.c - lines changed 463, context: html, text, full: html, text
• Updated the file comment in vcfBits.c/.h. No code change.
  • src/inc/vcfBits.h - lines changed 7, context: html, text, full: html, text
  • src/lib/vcfBits.c - lines changed 7, context: html, text, full: html, text