Collapsing linear paths, new test

[standage]

This PR introduces:

• A new test based on a 5bp deletion in the case relative to two controls. All existing tests only test for SNPs.
• Collapsing of linear paths associated with "interesting" k-mers. Often the linear path associated with one interesting k-mer is a subsequence of the linear path associated with a different interesting k-mer. These we can collapse trivially.

[standage]

kevlar find \
    --controls tests/data/trio1/ctrl?.counts \
    --case tests/data/trio1/case4.counts \
    --out novel.txt \
    --paths-out novel.paths \
    --ctrl_max 0 \
    --case_min 8 \
    tests/data/trio1/case4.fq

Try with/without the --collapse flag.

[standage]

Updated the scripts for simulating SNPs and indels to report small snippets of the mutated sequences, and updated the tests to test directly for these mutated snippets instead of for entire linear paths (which may change depending on sequencing errors, FP rate, etc.).

[standage]

Last week in this PR I started exploring different parameters a bit (k size, sequencing error rate, etc.) and integrating this into the automated test suite. However, this has crossed the line from testing to evaluation and analysis. These parameters are important to explore, but should not hold up work on implementing and evaluating the core algorithm.

I'm going to go ahead and merge this PR to that the deletion test and the linear path collapsing can be in master. I've opened up #21 as a placeholder for continued discussion.