jts/sga — pull request #74 by pradosj (2014-06-27 15:16:35+00:00)
Title: add kmer-count command

This is an implementation of a kmer-count command in SGA, inspired by the implementation of method extract in BWTTraverse.cpp. This new command is able to list the kmers of a BWT, and count the number of time they appears into another BWT. This can for example be useful to perform a variant calling, by listing the kmers from a readSet that are missing into another readSet.

The command is not parallelized, and I do not plane to implement this feature for the moment.