Mango using Partitioned parquet ADAM

[jpdna]

Replaces #358
works with ADAM: #1911

Example mango run

mango-submit --master yarn --num-executors 10 --executor-cores 8 --executor-memory 10g --driver-memory 20g  -- /home/eecs/akmorrow/builds/hg19.2bit -genes http://www.biodalliance.org/datasets/ensGene.bb -reads hdfs://{headnodepath}/user/jpaschall/mango1/HG00096_Jan30_v2.adam -show_genotypes

The problem with "chr" fix was resolved by querying both with and without "chr" prefix

[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/575/
Test FAILed.

[jpdna]

More recent test of this Mango code with partitioned dataset of the large Platinum genome files can be done with this 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/NA12877_S1.bam.partitioned.v3.adam,\
hdfs://amp-bdg-master.amplab.net:8020/user/jpaschall/feb16_work/NA12890_S1.bam.partitioned.v3.adam,\
hdfs://amp-bdg-master.amplab.net:8020/user/jpaschall/feb16_work/NA12889_S1.bam.partitioned.v3.adam\
-show_genotypes -parquetIsBinned

The "warm-up period", done upfront when using the -parquetIsBinned flag is still 30-45 sec one time, after that response time is 1-3 seconds when jumping around locations in genome browser,

[akmorrow13]

-parquetIsBinned -> isPartitioned

[jpdna]

This is replaced by #370