deBruijn graph for haplotype calling

[joergi-w]

This PR implements a deBruijn graph that can be used for calling haplotypes from short reads with respect to a reference sequence. Inline documentation and tests are included. The program that uses this data structure is supposed to perform the following steps:

• initialize an empty graph with a reference sequence
• add reads
• check whether the graph is viable (has enough unique kmers and no loops)
• prune nodes and edges with limited support
• retrieve the haplotype sequences

For debugging and other purposes, the graph can be exported into a formatted file, so it can be visualized with the dot program. I'm using the LEMON graph library for implementing the graph.

[codecov[bot]]

Codecov Report

Merging #217 (7973264) into master (64e5870) will increase coverage by 0.07%. The diff coverage is 99.09%.

@@            Coverage Diff             @@
##           master     #217      +/-   ##
==========================================
+ Coverage   98.40%   98.47%   +0.07%     
==========================================
  Files          18       20       +2     
  Lines         875      984     +109     
==========================================
+ Hits          861      969     +108     
- Misses         14       15       +1     

Impacted Files	Coverage Δ
src/structures/debruijn_graph.cpp	99.07% <99.07%> (ø)
include/structures/debruijn_graph.hpp	100.00% <100.00%> (ø)
src/variant_detection/snp_indel_detection.cpp	98.41% <0.00%> (-0.08%)	:arrow_down:
src/variant_detection/variant_output.cpp	100.00% <0.00%> (ø)

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