Permalink
Commits on Oct 11, 2010
  1. Fixed formatting

    committed Oct 11, 2010
  2. Obscured email address

    committed Oct 11, 2010
  3. Rewrote sga main webpage.

    committed Oct 11, 2010
  4. github generated gh-pages branch

    committed Oct 11, 2010
  5. Minor changes to the README

    committed Oct 11, 2010
  6. Added assert ScaffoldRecord::introduceGap to catch case where the exp…

    …ected overlap between scaffold components is not sane.
    committed Oct 11, 2010
  7. Bumped version to 0.92

    Changed usage message of main program to clearly indicate that the connect/scaffold commands are experimental.
    committed Oct 11, 2010
  8. Made the irreducible-edge only algorithm the default for sga overlap.…

    … All overlaps can be generated using the -x/--exhaustive option.
    committed Oct 11, 2010
  9. Implemented hybrid mode error correction which first performs a kmer …

    …correction pass, then overlap correction.
    
    Added parameters to the sga correct subprogram to control the kmer correction
    committed Oct 11, 2010
Commits on Oct 10, 2010
  1. More README updates

    committed Oct 10, 2010
  2. More dead code removal

    committed Oct 10, 2010
  3. Removed dead code from repository

    committed Oct 10, 2010
  4. Updated the README

    committed Oct 10, 2010
  5. Refactored repository to not contain data files and tools/analysis sc…

    …ripts. These are moved to the sgatools repo
    committed Oct 10, 2010
  6. Fixed bug in error corrector where no sequence would be output for un…

    …corrected reads in the kmer algorithm.
    
    Inlined the getDir function in the Edge class
    committed Oct 10, 2010
Commits on Oct 7, 2010
Commits on Oct 6, 2010
  1. Rewrote vertex/edge allocation logic so that a global memory pool is …

    …not used. The pool now belongs to the graph that creates the vertex/edge. This allows multiple graphs to be created in different threads without stomping over each other's memory. The global new for Vertex/Edges is disabled, the allocations must go through a pool.
    
    This commit was validated with valgrind - no memory leaks were found.
    committed Oct 6, 2010
Commits on Oct 5, 2010
Commits on Oct 4, 2010
  1. Updates on the sga2afg convertor script and the testing graphical fm-…

    …index python script
    committed Oct 4, 2010
Commits on Sep 30, 2010
Commits on Sep 21, 2010
Commits on Sep 20, 2010
  1. Initial checkin of sga2afg script

    committed Sep 20, 2010
Commits on Sep 16, 2010
Commits on Sep 10, 2010
  1. Added parameter to the correct subprogram to limit the amount of bran…

    …ching for complex reads.
    
    Added walk subprogram to extract the paths through the graph between two vertices
    Added scripts for coloring a graph with variants
    committed Sep 10, 2010
Commits on Sep 9, 2010
Commits on Sep 8, 2010
  1. Added depth filter to the error correct process to avoid correcting v…

    …ery deep sequences, which takes a lot of time.
    committed Sep 8, 2010
Commits on Sep 7, 2010
  1. Fixed seg fault in search where the m_pWalkIndex member of an SGWalk …

    …was not initialized in the copy constructor
    committed Sep 7, 2010
  2. Added some parameters to merge and correct. Moved the smoothing task …

    …in assemble to occur before simplification. Smoothing is still experimental.
    committed Sep 7, 2010