Reduce logging for the actual adamSave job

Conflicts:

	adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/rdd/AdamRDDFunctions.scala
Merge pull request #46 from nealsid/parquet-logging

Reduce logging for the actual adamSave job
SequenceDictionary adds containsRefName, updates recordName key types.

Added containsRefName to SequenceDictionary, allowing us to check whether a SequenceDictionary object contains a particular sequence.
SequenceDictionary recordNames keys should be Strings (they had been Avro Utf8 objects, which was messing up lookups into the map itself from Strings).
Merge pull request #47 from genomebridge/tdanford/seq-dict-contains-ref

Adding containsRefName to SequenceDictionary
Update Spark to 0.8.1 and add hadoop2.2 profile
Merge services files when building assembly JAR
Use '\t' instead of ',', as , is a valid character
Merge pull request #52 from genomebridge/attributesSeparator

Attributes: Use '\t' instead of ',', as , is a valid character
Wholeheartedly make Hadoop 2.2.0 the default
Add explicit dependency on scala-library 2.9.3
Merge pull request #53 from jey/hadoop22-fix

Fix Hadoop 2.2.0 support, upgrade to Spark 0.8.1
[maven-release-plugin] prepare release adam-parent-0.6.0
[maven-release-plugin] prepare for next development iteration
Adding Yy as base in MdTag
Merge pull request #56 from arahuja/mdtag

Adding Yy as base in MdTag
Adding reads to rods transformation.
Merge pull request #36 from bigdatagenomics/reads-to-rods

Adding reads to rods transformation.
Parse read groups and create mapping from bam/sam header
Merge pull request #48 from arahuja/readgroupsmapping

Parse read groups and create mapping from bam/sam header
fix index and remove rdd arguments