File Changes for kent

v277_base to v278_preview (2012-12-18 to 2013-01-08) v278

• src/kehayden/alphaAsm/alphaAsm.c
  • lines changed 130, context: html, text, full: html, text
    Starting work on a second pass of processing to put in monomers that did not get omitted by main pass.
  • lines changed 29, context: html, text, full: html, text
    Adding a new check on input.
  • lines changed 13, context: html, text, full: html, text
    More progress towards substituting in missing monomers.
  • lines changed 158, context: html, text, full: html, text
    Fixing end condition in matchExceptCenter. Rearranging debugging code.
  • lines changed 61, context: html, text, full: html, text
    Adding fall back logic to place unused monomers by type if they can't be placed by context.
  • lines changed 32, context: html, text, full: html, text
    Making subCenterInNeighborhood routine work on a wider variety of input and putting in some additional logging/debugging options.