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Commits on May 7, 2020

• Update submodules and wrapper

  rvaser

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Commits on Mar 10, 2020

• flush print message in wrapper

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  SHuang-Broad

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Commits on Mar 7, 2020

• racon_wrapper supports gpu options

  SHuang-Broad

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Commits on Nov 21, 2019

• Add paired-end preprocessing script

  rvaser

  committed
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Commits on Apr 23, 2018

• Fixed usage and README

  rvaser

  committed
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Commits on Apr 5, 2018

• Changed path of work directory in wrapper and fixed the destructor

  rvaser

  committed
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Commits on Mar 27, 2018

• Updated error messages in wrapper

  rvaser

  committed
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Commits on Mar 8, 2018

• Added submodule rampler, implemented racon wrapper, updated fragment correction to expect dual overlaps, added SAM tags to headers of polished targets, updated README and unit tests

  rvaser

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Commits on Feb 2, 2018

• Cleaned repository

  rvaser

  committed
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Commits on Aug 8, 2016

• Updated the shebang lines in Python scripts.

  isovic

  committed
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Commits on Jun 7, 2016

• Created the initial version of the error correction option. Changed the commandline to expect MHAP as default, and require the reads file at all times.

  isovic

  committed
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Commits on Jun 1, 2016

• Updated the evalcontigs.py debug output. Now a file is generated with all frags.

  isovic

  committed
  b7e6c01

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• Minor syntax error fix.

  isovic

  committed
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Commits on May 31, 2016

• Handled a case when there were no frags for a contig in evalcontigs.py.

  isovic

  committed
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• Updated the output of evalcontigs.sh script.

  isovic

  committed
  17a7f8e

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• Updated the output of evalcontigs.sh script.

  isovic

  committed
  e508e4d

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• Updated the output of evalcontigs.sh script.

  isovic

  committed
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• Added a --silent flag to evalcontigs.py.

  isovic

  committed
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• Added a script to evaluate contigs in a simple but effective manner. The script takes the input contigs file, takes each contig separately and maps it to the reference using nucmer, piped with delt…

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  isovic

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Commits on May 29, 2016

• Added the modified paf2mhap.pl script

  isovic

  committed
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• This should be a functional version of the MHAP consensus. Tested on Lambda and E. Coli MAP006 datasets, now going to test it on something larger.

  isovic

  committed
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Commits on May 24, 2016

• Modified edcontigs.py to include the unaligned bases into the edit distance.

  isovic

  committed
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• Fixed an issue with the edit distance script. When there was only one fragment reported by dnadiff, it would break if it was a reverse complement.

  isovic

  committed
  2cfe773

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• Added a check for empty subsequences. Fixed a relative path issue for a temp folder in edcontigs.py.

  isovic

  committed
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Commits on May 18, 2016

• Removed excess files.

  isovic

  committed
  6b9d4ba

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• Fixed the wrong path for real now.

  isovic

  committed
  9a89f23

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• Fixed wrong samscripts path.

  isovic

  committed
  018f9c5

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• Fixed a missing script issue.

  isovic

  committed
  971bfc1

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• Cleaned the code up a bit.

  isovic

  committed
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Commits on May 17, 2016

• Added a filter for overhangs in windows.

  isovic

  committed
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Commits on May 3, 2016

• consensus.cc now creates a fatal crash if a window is empty, also if there are 2 or less sequences in the window, the first one is output instead of their 'consensus'.

  isovic

  committed
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Commits on Apr 30, 2016

• Minor changes.

  isovic

  committed
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• Added an interval tree implementation to the gfacons.py script to speed up alignment of individual reads.

  isovic

  committed
  5b7e2ba

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• Fixed a bug with the last window, where the reads would not get trimmed properly, causing the last window to take a long time to align. Added Edlib as a submodule for evaluating the consensus resul…

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  isovic

  committed
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Commits on Apr 29, 2016

• Fixed an issue with path to GraphMap and the reference name.

  isovic

  committed
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