This modules performs the first step of Mapsembler2.
For each starter, it outputs a list of "substaters" consisting of extremities of the starter that are found in the reads, up to 1 indel or mismatch
the algorithm goes as follows:
for each starter;
for each kmer u at the extremity of this starter
for each k-mer u' where u' is u with an indel or a subsitution or just u
see how many times u' is in the reads
if u' is present more than M times (M=3 by default)
then output u' as a extremal substarter for this starter
# Project build
For building your project, you should do the following
mkdir build; cd build; cmake ..; make
Then, you should get a binary holding the name of the project.
Note: the first compilation should take some time since the GATB-CORE library is generated.