Minor misc updates
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Banding approach for PairHMM utility class. Adds bands to a work queue when distinct likelihood masses are detected in the HMM matrices. Works over a wide range of haplotype sizes and GOP values.
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Moving trimToVariableRegion out of reduced reads and into a public static ReadClipper function. HaplotypeCaller clips reads to the active region boundries before passing to the HMM. The philosophy of the HC is moving towards genotyping the entire haplotype sequence contained within the active region as a single allele.
updating HaplotypeCaller integration tests
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
analyzeRunReports cleanup for new minimal GATKRunReport structure

-- No more command lines or working directories
-- Added failing and successful gatkrunreports to public/testdata for testing
Bugfix for analyzeRunReports.py: now handles case where hostname is missing
Don't assume files have .bai and .bas associated with them
Updated the bundle to use the official filtered (final) indel calls
Updating dbsnp to v135
Generalizing to avoid JDK 1.7 incompatibilities
Fix old error message
GATKReport v1.0

GATKReport format changes:

 - All non-data header lines are preceeded with a single pound ( #:)
 - Every report now has a report header containing the version number and number of tables
 - Every table has two lines of table header: The first explains the size of the table and the data types of each column, the second contains the table name and description.
 - This new format will allow reports in the future to be gatherable.
 - Changed the header format to include an end-of-line string ":;"

Added features:

 - Simplified GATK Reports:

	The constructor for a simplified GATK Report. Simplified GATK report are designed for reports that do not need the advanced functionality of a full GATK Report.

	A simple GATK Report consists of:
		- A single table
		- No primary key ( it is hidden )
	    Optional:
		- Only untyped columns. As long as the data is an Object, it will be accepted.
		- Default column values being empty strings.
	Limitations:
		- A simple GATK report cannot contain multiple tables.
		- It cannot contain typed columns, which prevents arithmetic gathering.

       - Added a constructor to generate simplified GATK reports.
       - Added a method to easily add data to simple GATK reports.

 - Upgraded the input parser take advantage of the new file format (v1).
 - Added the GATKReportGatherer, more usability cmoing in next versionof GATK Report. Curently, it can only add rows from one table to another. Added private methods in GATKReport to combine Tables and Reports, It is very conservative and will only gather if the table columns, as well as everything else matches. At the column level, it uses the (redundant) row ids to add new rows. It will throw an exception if it is overwriting data.
 - Made some GATKReport methods public, and added more setters and getters.
 - Added method that compares formats of two GATKReports, and added an equals method to verify all data inside.
 - The gsalib for R now supports reading GATKReport v1 files in addition to legacy formats (v0.*)
 - Added a GATKReportDataType enum to give column a certain data type. This must be specified when making a gatherable report. This enum contains several methods including a reverse lookup map.
 - Added a data type field in GATKColumn, when a type is not specified, the unknown type is used. Unknown types should not be gathered.

Test changes:

 - Updated Unit Tests for GATK Report v1. Added a test for the gatherer. Left one test disabled while we transition from v0 to v1.
 - Updated the MD5 hashes in integration tests throughout the GATK.

Other changes:

 - Added the gatherer functions to CoverageByRG
 - Also added the scatterCount parameter in the Interval Coverage script
 - Dropped support for reading in legacy GATKReport formats ( v0.*)
 - Updated VariantEvalWalker to work with GATK Report v1, added a format String to all applicable DataPoints.
 - Rewrote the read file method for GATK report files.
 - Optimized the equals methods within GATKReport. The protected functions should only be called by the GATKReport methods.

Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Unfortunately need to bump up memory needed for liftover to get Omni file sorted
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Restoring key-related unit/integration tests

The recent GATKReport commit accidentally clobbered a few tests -- this
restores them.
Generalized runtime simplifying routines in analyzeRunReports

-- Handles 2012/3/12 as well as 2012-3-12
-- UnitTests to test it's working correctly
quick todo for next time we make a bundle