Commits for tdreszer

v278_base to v279_preview (2013-01-22 to 2013-01-29) v279

• Added local memeory support for bits and a couple of routines to query lm size.
  • src/inc/bits.h - lines changed 23, context: html, text, full: html, text
  • src/inc/localmem.h - lines changed 19, context: html, text, full: html, text
  • src/lib/bits.c - lines changed 69, context: html, text, full: html, text
  • src/lib/localmem.c - lines changed 56, context: html, text, full: html, text
• Checking in 'elmTree' which uses neighbor joining to build a tree in local memory. Also checking in 2 sets of changes to vcf. First, added support for a 'reuse' local memory pool which aid traversing giant files. Second, added routines for bitmap based analysis of variants.
  • src/inc/elmTree.h - lines changed 122, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 147, context: html, text, full: html, text
  • src/lib/elmTree.c - lines changed 275, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 571, context: html, text, full: html, text
• Targeted change to fetchCodons() to avoid seg fault when calculated sequence length is less than or equal to zero.
  • src/hg/lib/pgSnp.c - lines changed 7, context: html, text, full: html, text