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

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

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

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    …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

    authored
    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…

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    … 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

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

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

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

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

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

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

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    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

    Merge github.com:jts/sga

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

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  2. Incremented version to 0.9.9.

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    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…

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    …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…

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

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