[AVOCADO-257] Add ability to discard mate info for mates on filtered contigs

[fnothaft]

Resolves #257.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/203/
Test PASSed.

[coveralls]

Coverage decreased (-0.3%) to 81.673% when pulling 455e32b on fnothaft:issues/257-mate-filtered-contig into 5f720cf on bigdatagenomics:master.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/avocado-prb/204/
Test PASSed.

[coveralls]

Coverage decreased (-0.07%) to 81.891% when pulling 6df7f2d on fnothaft:issues/257-mate-filtered-contig into 5f720cf on bigdatagenomics:master.