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Commits on Jun 17, 2011
  1. Implemented extension mode for sga cluster. This required refactoring…

    … the SequenceProcessFramework to use a generic generator object.
  2. Refactored cluster generation code into ReadCluster class. Added stub…

    … subprogram for cluster-extend.
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.
Commits on Jun 14, 2011
Commits on Jun 10, 2011
  1. Merge pull request #7 from avilella/master

    a small typo in a cerr
  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.
Commits on Jun 5, 2011
  1. Fixed gcc 4.6 compile warnings

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

  2. Added std::map-based ScaffoldSequenceCollection for scaffolding seque…

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

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

  5. sga scaffold: allow loading sequences with ambiguity codes, disable t…

    …he requirement that an a-statistic file is provided.
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
  2. @avilella

    deleting INSTALL for now

    avilella authored
  3. @avilella

    walk with prefix tweak

    avilella authored
  4. @avilella
  5. @avilella

    reverting to original walk

    avilella authored
  6. @avilella


    avilella authored
  7. @avilella
Commits on May 31, 2011
  1. Updated main README file.

  2. 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)
Commits on May 30, 2011
  1. 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.
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
  2. Implemented caching of BWTIntervals for all strings of a given length…

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