Commits on Feb 7, 2011
  1. Updated version to 0.9.5

    committed Feb 7, 2011
Commits on Feb 4, 2011
  1. Added function to break the scaffold graph at positions that have con…

    …flicting distance estimates.
    Also changed the link validator to break the graph when invalid links are found instead of deleting one of the vertices.
    committed Feb 4, 2011
  2. Changed scaffold2fasta to write out unplaced scaffolds and use a gap …

    …with a minimum length
    committed Feb 4, 2011
Commits on Feb 3, 2011
  1. Minor formatting tweaks.

    committed Feb 3, 2011
Commits on Feb 2, 2011
Commits on Feb 1, 2011
  1. Fixed scaffold2fasta to search for a path of the correct length (was …

    …using end to start distance instead of end to end).
    First pass at removing contigs from scaffold graph that do not have consistent distance estimates.
    committed Feb 1, 2011
Commits on Jan 31, 2011
  1. Rewrote FMMergeProcess to use the compare-and-swap functionality in t…

    …he bit vector. Removed the locks.
    committed Jan 31, 2011
  2. Changed name of cigar line in variants file to make it clear its an i…

    …nternally-used field and not for the fasta sequence that is output.
    committed Jan 31, 2011
  3. Integrated Heng Li's stdaln dynamic programming library into ThirdPar…

    …ty. This is used in the variation removal algorithm to set an upper bound on how different two sequences can be and still be removed.
    It was found that the previous code would collapse together very divergent pieces of unique sequence by finding a path between two different low-copy repeats. This is clearly undesirable.
    committed Jan 31, 2011
Commits on Jan 30, 2011
  1. Removed some prints

    committed Jan 30, 2011
  2. First implementation of new scaffolding algorithm.

    Now generates primary scaffold but does not do much error checking or attempt to place small contigs in the gaps.
    committed Jan 30, 2011
  3. Wrote algorithm to compute a layout of the connected component for a …

    …scaffold starting from a terminal vertex. This function is the backbone of the scaffolding algorithm.
    committed Jan 30, 2011
Commits on Jan 29, 2011
Commits on Jan 28, 2011
Commits on Jan 27, 2011
  1. Cleaned up code

    committed Jan 27, 2011
  2. Added new function to remove transitive edges from the scaffold graph…

    …. Needs more work.
    committed Jan 27, 2011
Commits on Jan 25, 2011
  1. Removed some dead code.

    committed Jan 25, 2011
  2. Simplified construction of variation paths in the graph. More work on…

    … making the searching code more generic.
    committed Jan 25, 2011
Commits on Jan 24, 2011
  1. Made the SGSearchTree a generic templated class so that it can also b…

    …e used for the scaffolding module.
    committed Jan 24, 2011
Commits on Jan 21, 2011
  1. Added functions to compute the probability that two scaffold links ar…

    …e incorrectly ordered.
    committed Jan 21, 2011
Commits on Jan 20, 2011