New AdamContext and RichAdamRecord decorators. New RDD methods. Schema fixes.

o Created a new AdamContext decorator for SparkContexts with methods for
  creating new ADAM RDDs from SAM/BAM or ADAM files
o New methods added to RDDs created by ADAM for aggregating pileups, sorting, and
  saving. Makes it easy to compose transformations, e.g. rdd.sort().markDups().save()
o Added new 'RichAdamRecord' decorator for ADAMRecords with useful utility methods
o Fixed a 1-off bug in mateReferencePosition. All offsets are now 0-based.
o Removed the 'end' field from an ADAMRecord and added 'mateReferenceId'
Fix case-sensitivity issue with last commit
Exclude the Eclipse Java development tools from shaded jar
Improve the performance of ReferencePosition.compare()
Remove the Hadoop-BAM source and use new binary artifacts instead

The Hadoop-BAM team is now publishing Maven actifacts for their
project so there's no reason to have the source in the ADAM repo
anymore. The latest version of Hadoop-BAM fixes a bug when splitting
BAM files and also provides Hadoop 1/2 support via reflection.
Split bam2adam command into 'bam2adam' and 'transform' commands

Previously, the 'bam2adam' command read BAM files using a Hadoop FileInputFormat,
performed one or more transforms and then save the transformed data to ADAM
format. This required the FileInputFormat to deal with the BGZF block compression
markers to find splits which was too error prone. We may revisit this in the
future.

Now, the 'bam2adam' command reads a BAM file locally using the SAMFileReader in
samtools and saves the ADAM/Parquet to the URI specified (e.g. hdfs://, s3://, local).
This command will be improved in the future batch entire directories of files
and support partitioning.

The new 'transform' command reads an ADAM/Parquet file, performs one or more
transformations in-memory and then saves the result to a new ADAM/Parquet file.

Additionally,
o Updated the version of samtools from 1.93 to 1.96-1534 per Chris Hartl's request
  to support his work on Base Quality Score Recalibration
o Dropped dependencies on Hadoop-BAM and Picard
Make the samtools validation 'lenient' by default