bigdatagenomics/avocado — pull request #56 by fnothaft (2014-04-28 17:55:58+00:00)
Title: Parametrize flanking sequence length for k-mer graph creation

Updated de Brujin graph generation code to allow users to specify the amount of flanking sequence to use. This is necessary as graph creation fails if there is a SNP/read error that overlaps with the first _k_-mer in the flanking reference.

Additionally:

* Imported test-jar from ADAM, to get SparkFunSuite
* Added code for exporting KmerGraph to Dot/Graphviz format for debug/visualization
* Added small test SAM file from NA12878