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Commits on Oct 15, 2010
  1. Cleaned up help message for many subprograms, mostly by adding defaul…

    …t parameters.
    
    Changed -t,--trim option in sga assemble to -x,--cut-branches to avoid confusion with --threads used elsewhere.
    committed Oct 15, 2010
  2. Extended --permuteN option in preprocess to handle the full IUPAC amb…

    …iguity code set as suggest by Shaun Jackman.
    
    The option has been renamed --permute-ambiguous
    committed Oct 15, 2010
  3. Modified SeqReader to automatically uppercase all input sequences.

    Added validation flag to SeqReader to detect when non-ACGT characters are present in the reads. This condition will trigger an error in all programs except for sga preprocess.
    committed Oct 15, 2010
Commits on Oct 14, 2010
Commits on Oct 13, 2010
  1. add rmdup-pe workflow to sga-pipeline to remove duplicated paired-end…

    … reads
    
    added sga-joinedpe helper script to join/split PE read files
    committed Oct 13, 2010
Commits on Oct 12, 2010
  1. Added pipeline script information to the README

    Updated comments in bin/sga-pipeline
    committed Oct 12, 2010
  2. Added bin directory with first version of sga-pipeline script

    Added option to overlap and rmdup subprograms to specify output file
    committed Oct 12, 2010
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
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