Initial commit
Initial commit
Update the README
Improved build, added license, file converters, module framework and README.
Parquet, Hadoop-BAM integration, Hadoop 1/2 support

o ADAM now generates Avro records and stores them in Parquet files.
o Conversion from genomic file formats to Avro is now done using
  Hadoop Map-Reduce (instead of only local)
o ADAM now runs with any version of Hadoop
o Support for FASTA files has been added
o Cleaned up the way Avro generate source is handled
o Added optional BAM attributes to ADAM format
Add a simple pig script example
FastaInputFormat should have isSplitable() return false always
New pileup and faster print command

NEW FEATURES

  New pileup command that creates a reference-ordered data file sorted
  by position with the reference base and pileup (including phred scores)
  at each position

IMPROVEMENTS

  The print command is simplified and no longer launches a map-reduce job.
  Contents of files are now immediately streamed to console.

  Added the unique record group identifier to ADAM read records

BUG FIXES

  Fixed the read file format to use 0-based (instead of 1-based) offsets
  for read positions. All ADAM files are 0-based.
Convert the project to a multi-module project

This change will make it easier to publish artifacts targetted
at integration with other systems like GATK.
Added record for format used to describe variants being called.
Merge pull request #1 from fnothaft/master

Added record for format used to describe variants being called.
Ported ADAM to use Apache Spark

o Using Spark for MR instead of Hadoop
o Renamed the flag fields and fixed the way they are set (using default of false for null)
o New pileup -- lots of work here
o Using Parquet predicate pushdown
o Increased default block size from 50MB to 256MB
No longer needed
Add event offset and length to the pileup format
Separate read processor into separate to class prevent shipping entire reads2ref command
Create a new ParquetFileTraversable class to simplify reading Parquet
Draft implementation of a pileup traversable. Mpileup command.
Added map/Sanger quality scores to Pileup.
Making fixes to pull request.
Merge pull request #2 from fnothaft/master

Added map/Sanger quality scores to Pileup.