merging conflicts within:

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

Conflicts:
	adam-commands/pom.xml
	adam-commands/src/main/scala/edu/berkeley/cs/amplab/adam/AdamMain.scala
	adam-commands/src/main/scala/edu/berkeley/cs/amplab/adam/rdd/AdamContext.scala
	pom.xml
Make the samtools validation 'lenient' by default
Moltenized version of a Variant/Genotype pair - ADAMVariantGenotype. This record contains all the reserved keys for VCF, plus a few extra convenience keys for typical kinds of groupings.

In addition, schema for standalone Genotype records and Variant records. It should be that ADAMDiploidGenotype objects can simply fold into an ADAMVariant and update the statistics. These records introduce the concept of likelihood bounding to overcome the necessity to refer back to all of the alternate alleles at the site level. In this way, site-level VCFs can be reconstructed from genotype objects without losing any resolution except on the least-likely genotype states.
Some changes to ADAMVariant