[CANNOLI-65] Adding Snap for alignment.

[heuermh]

Fixes #65. Adapted from fnothaft@e5ba4f4.

Work in progress. The default docker image has an ENTRYPOINT defined,

ENTRYPOINT ["/opt/SNAP/snap-aligner"]

which causes trouble for Cannoli

INFO  SnapFn:98 - Piping RDDBoundFragmentRDD with
0 reference sequences, 0 read groups, and 0 processing steps to snap with
command: [docker, run, -i, -v, /Users/heuermh/working/cannoli:/Users/heuermh/working/cannoli,
--rm, quay.io/ucsc_cgl/snap:1.0beta.18--07475052cd34f17055991cec339898ff0e8bd07d,
snap-aligner, paired, /Users/heuermh/working/cannoli/hla.fa, -t, 1,
-pairedInterleavedFastq, -, -o, -bam, -, -map, -pre] files: []
...
new name: H06HDADXX130110:2:2116:3345:91806/1
new name: H06HDADXX130110:2:2116:3345:91806/2
new name: H06HDADXX130110:1:2103:11970:57672/1
new name: H06HDADXX130110:1:2103:11970:57672/2
new name: H06JUADXX130110:1:1108:6424:55322/1
new name: H06JUADXX130110:1:1108:6424:55322/2
Welcome to SNAP version 1.0beta.18.

Invalid command: snap-aligner

Usage: snap <command> [<options>]
Commands:
   index    build a genome index
   single   align single-end reads
   paired   align paired-end reads
   daemon   run in daemon mode--accept commands remotely
Type a command without arguments to see its help.

Also not sure which file(s) from the index directory need to be copied using the SparkFiles mechanism.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/cannoli-prb/132/
Test PASSed.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/cannoli-prb/137/
Test PASSed.

[coveralls]

Coverage increased (+0.9%) to 22.397% when pulling e59078f on heuermh:snap into 4ea7617 on bigdatagenomics:master.

[heuermh]

Also needs updating per #132.

[heuermh]

Closing as WontFix