Commits on Apr 18, 2011
  1. bumped version number

    committed Apr 18, 2011
  2. Made the maximum distance estimate error when resolving gaps a comman…

    …d line parameter
    committed Apr 18, 2011
Commits on Apr 11, 2011
  1. Bumped version to 0.9.6

    committed Apr 11, 2011
  2. [Github issue 4] Made the error message for the case where a substrin…

    …g read is found during string graph construction to be more informative.
    committed Apr 11, 2011
Commits on Mar 7, 2011
Commits on Mar 4, 2011
  1. Changed sga-cluster so the temp file uses the same prefix as the -o p…

    …arameter to prevent name clashes.
    committed Mar 4, 2011
  2. Changed sga-scaffold arguments. Unified repeat/unique a-stat so any c…

    …ontig that does not meet the unique cutoff is deemed to be a repeat. Added --min-copy-number parameter to discard contigs that have a low (<0.3) estimated copy number.
    committed Mar 4, 2011
Commits on Mar 3, 2011
Commits on Mar 1, 2011
  1. Bug fix in ScaffoldRecord to avoid outputting duplicate records for s…

    …ingleton scaffolds.
    committed Mar 1, 2011
Commits on Feb 28, 2011
  1. Removed the default seed stride parameter for sga-cluster as it would…

    … lead to some overlaps being missed.
    committed Feb 28, 2011
Commits on Feb 27, 2011
  1. Added new filtering modes to sga-filterBAM. Can now filter out pairs …

    …based on error rate, mapping quality and kmer depth.
    committed Feb 27, 2011
Commits on Feb 26, 2011
  1. Fixed warning in OverlapBlock

    committed Feb 26, 2011
Commits on Feb 23, 2011
  1. Fixed tripped assertion in makeScaffolds for the very rare case that …

    …a terminal vertex cannot be found. Fixed stats output to avoid 32-bit integer wraparound.
    committed Feb 23, 2011
Commits on Feb 21, 2011
  1. Fixed usage message for scaffold.

    committed Feb 21, 2011
  2. Added exit statement to when the the command line argum…

    …ents are incorrect.
    committed Feb 21, 2011
Commits on Feb 20, 2011
Commits on Feb 19, 2011
  1. Made the kmer corrector the default algorithm to use for sga-correct.…

    … Changed the default kmer size to 31.
    committed Feb 19, 2011
  2. Changed the error correction metrics to use wider integers to avoid w…

    …rap arounds for very large data sets.
    committed Feb 19, 2011
  3. Added -w parameter to sga-walk to allow the exact sequeunce of the wa…

    …lk to be specified.
    committed Feb 19, 2011
  4. Added the contigs filename to the temporary output of bwa aln so the …

    …same reads can be mapped to different contigs at the same time without having a filename clash.
    committed Feb 19, 2011
Commits on Feb 17, 2011
  1. Wrote experimental program sga-cluster to write out the connected com…

    …ponents of a graph. Requested by Albert Vilella.
    committed Feb 17, 2011
Commits on Feb 15, 2011
  1. Rewrote the exact-mode irreducible block algorithm to be iterative in…

    …stead of recursive.
    committed Feb 15, 2011