Use Hive-style partitioning

[jpdna]

Replaces #361

Works with ADAM PR bigdatagenomics/adam#1922

Reading partitioned files works, for example with command

mango-submit --master yarn --num-executors 10 --executor-cores 4 --executor-memory 20g --driver-memory 20g  -- /home/eecs/akmorrow/builds/hg19.2bit -genes http://www.biodalliance.org/datasets/ensGene.bb -reads hdfs://amp-bdg-master.amplab.net:8020/user/jpaschall/feb16_work/NA12889_S1.bam.partitioned.v4_withpartnum.adam -show_genotypes -parquetIsBinned

Note, this PR currently fails tests, but so does Mango Master for me at, 328b519
I get test failure

VizReadsSuite:
2018-02-25 16:29:33 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
*** RUN ABORTED ***
  java.lang.NoClassDefFoundError: org/apache/http/ssl/SSLContexts
  at org.apache.http.impl.client.HttpClientBuilder.build(HttpClientBuilder.java:966)
  at org.scalatra.test.HttpComponentsClient$class.createClient(HttpComponentsClient.scala:99)
  at org.bdgenomics.mango.cli.VizReadsSuite.createClient(VizReadsSuite.scala:27)
  at org.scalatra.test.HttpComponentsClient$class.submit(HttpComponentsClient.scala:62)
  at org.bdgenomics.mango.cli.VizReadsSuite.submit(VizReadsSuite.scala:27)

[AmplabJenkins]

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/mango-prb/607/
Test FAILed.

[jpdna]

This worked fine with, ADAM with the PR bigdatagenomics/adam#1948
at
f745bca

Note, you need to use partitioned parquet files generated from that version of the ADAM PR.
This works:

../mango/bin/mango-submit --master yarn --num-executors 10 --executor-cores 4 --executor-memory 20g --driver-memory 20g  -- ./hg19.2bit -genes http://www.biodalliance.org/datasets/ensGene.bb -reads hdfs://amp-bdg-master.amplab.net:8020/user/jpaschall/march9/NA12877_S1.partitioned.v2.adam  -show_genotypes 

[akmorrow13]

Jenkins, retest this please.

[AmplabJenkins]

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/mango-prb/623/
Test PASSed.

[akmorrow13]

@jpdna can you add unit tests?

[AmplabJenkins]

Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins//job/mango-prb/624/
Test PASSed.

[akmorrow13]

remove empty line

[akmorrow13]

remove empty line

[akmorrow13]

This looks great @jpdna ! Just some minor spacing comments, otherwise it looks good to go on my side.

[akmorrow13]

Replaced with #379