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Commits on Jun 14, 2016
  1. Updating to Opal v3.1.b0

    danfdeblasio committed Jun 14, 2016
    Includes some updates to clean up the debugging output for adaptive
    local realignment and handle the output of files more smoothly.
Commits on Mar 2, 2016
  1. Bug Fix

    danfdeblasio committed Mar 2, 2016
Commits on Feb 18, 2016
  1. Typo

    danfdeblasio committed Feb 18, 2016
  2. Spelling Error

    danfdeblasio committed Feb 18, 2016
Commits on Feb 1, 2016
Commits on Jan 25, 2016
  1. bug fixes

    danfdeblasio committed Jan 25, 2016
  2. Argument Cleanup & Itterations

    danfdeblasio committed Jan 25, 2016
    Cleaning up how realignment arguments are input and adding realignment
    iteration.
Commits on Jan 12, 2016
Commits on Jan 7, 2016
Commits on Jan 6, 2016
  1. small bug fix

    danfdeblasio committed Jan 6, 2016
Commits on Jan 5, 2016
  1. errors in realignment

    danfdeblasio committed Jan 5, 2016
  2. Merge pull request #2 from danfdeblasio/realignment

    danfdeblasio committed Jan 5, 2016
    Realignment
  3. Merge pull request #1 from danfdeblasio/lopsided_terminals

    danfdeblasio committed Jan 5, 2016
    Lopsided terminals
  4. Merge branch 'lopsided_terminals' into realignment

    danfdeblasio committed Jan 5, 2016
    # Conflicts:
    #	.gitignore
    #	opal/IO/ArgumentHandler.java
    #	opal/IO/Configuration.java
    #	opal/IO/Inputs.java
    #	opal/Opal.java
    #	opal/realignment/realignmentDriver.java
  5. Pre-Merge from Lopsided

    danfdeblasio committed Jan 5, 2016
Commits on Jan 4, 2016
Commits on Dec 21, 2015
Commits on Dec 17, 2015
Commits on Dec 4, 2015
  1. remove blank lines

    danfdeblasio committed Dec 4, 2015
    remove blank lines in realignment rather than ignore those regions
Commits on Dec 1, 2015
  1. Initial Realignment Code

    danfdeblasio committed Dec 1, 2015
    This includes a simplified (untested) version of realignment that
    ignores any terminal gap costs, has a fixed window size at 5, and a
    minimum block size of 10. Two passes remove any saved blocks smaller
    than 10, then saves any realignment regions less than 10 columns.
Commits on Aug 27, 2015
  1. Minor bugs

    danfdeblasio committed Aug 27, 2015
Commits on Jul 20, 2015
  1. Adding back com

    danfdeblasio committed Jul 20, 2015
  2. Some updates on this end

    danfdeblasio committed Jul 20, 2015