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Commits on Jun 17, 2011
  1. Fixed formatting of sga cluster help

    committed Jun 17, 2011
  2. Implemented extension mode for sga cluster. This required refactoring…

    … the SequenceProcessFramework to use a generic generator object.
    committed Jun 17, 2011
  3. Refactored cluster generation code into ReadCluster class. Added stub…

    … subprogram for cluster-extend.
    committed Jun 17, 2011
Commits on Jun 15, 2011
  1. Added early exit to kmerCorrect when the read sequence is shorter tha…

    …n the kmer length.
    Thanks to Dan Hughes for the bug report and test case.
    committed Jun 15, 2011
Commits on Jun 14, 2011
Commits on Jun 10, 2011
  1. Merge pull request #7 from avilella/master

    a small typo in a cerr
    committed Jun 10, 2011
  2. @avilella
Commits on Jun 7, 2011
  1. Check sem_init return codes to catch errors when this function is not…

    … implemented (on OSX). This is a stop-gap measure until I have time to switch to named semaphores.
    committed Jun 7, 2011
Commits on Jun 5, 2011
  1. Fixed gcc 4.6 compile warnings

    committed Jun 5, 2011
Commits on Jun 4, 2011
  1. Handle Ns in Util::complement

    committed Jun 4, 2011
  2. Added std::map-based ScaffoldSequenceCollection for scaffolding seque…

    …nces that do not belong to a graph.
    committed Jun 4, 2011
  3. Factored out the scaffold input sequence container into ScaffoldSeque…

    …nceCollection so that it does not require using a StringGraph
    committed Jun 4, 2011
  4. Changed wording in a-stat warning

    committed Jun 4, 2011
  5. sga scaffold: allow loading sequences with ambiguity codes, disable t…

    …he requirement that an a-statistic file is provided.
    committed Jun 4, 2011
Commits on Jun 3, 2011
  1. Merge pull request #6 from avilella/master

    merging change by avilella to allow the sequences output by sga walk to have a user-defined prefix
    committed Jun 3, 2011
  2. @avilella

    deleting INSTALL for now

    avilella committed Jun 3, 2011
  3. @avilella

    walk with prefix tweak

    avilella committed Jun 3, 2011
  4. @avilella
  5. @avilella

    reverting to original walk

    avilella committed Jun 3, 2011
  6. @avilella


    avilella committed Jun 3, 2011
  7. @avilella
Commits on May 31, 2011
  1. Updated main README file.

    committed May 31, 2011
  2. Tweaked wording in top-level README

    committed May 31, 2011
  3. Incremented version to 0.9.9.

    This version includes running-time improvements including:
    -an interval pre-computation scheme to reduce the time required when performing k-mer interval lookups
    -the ability to suppress construction of the reverse FM-index (when performing k-mer correction)
    committed May 31, 2011
Commits on May 30, 2011
  1. Added a directory with sga examples. Currently holds a script for a c…

    …. elegans assembly.
    committed May 30, 2011
  2. Added option to sga-index to suppress constructing the reverse BWT. M…

    …odified sga-merge to avoid attempting to merge RBWTs if they don't exist.
    This new option is useful when performing k-mer correction as the RBWT is no longer used.
    committed May 30, 2011
Commits on May 29, 2011
  1. Code cleanup: created a parameter object for setting the error correc…

    …tion options in place of a constructor with many arguments
    committed May 30, 2011
  2. Implemented caching of BWTIntervals for all strings of a given length…

    …. Currently used in the k-mer corrector.
    committed May 29, 2011
Commits on May 28, 2011
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