Merge pull request #43 from broadinstitute/md_qualutils_cleanup

Cleanup of QualityUtils
Reducing the size of the reference padding in the HaplotypeCaller.
Merge pull request #44 from broadinstitute/rp_hc_reference_padding
ActivityProfile and ActiveRegions respects engine interval boundaries

-- Active regions are created as normal, but they are split and trimmed to the engine intervals when added to the traversal, if there are intervals present.
-- UnitTests for ActiveRegion.splitAndTrimToIntervals
-- GenomeLocSortedSet.getOverlapping uses binary search to efficiently in ~ log N time find overlapping intervals
-- UnitTesting overlap function in GenomeLocSortedSet
-- Discovered fundamental implementation bug in that adding genome locs out of order (elements on 20 then on 19) produces an invalid GenomeLocSortedSet.  Created a JIRA to address this: https://jira.broadinstitute.org/browse/GSA-775
-- Constructor that takes a collection of genome locs now sorts its input and merges overlapping intervals
-- Added docs for the constructors in GLSS
-- Update HaplotypeCaller MD5s, which change because ActiveRegions are now restricted to the engine intervals, which changes slightly the regions in the tests and so the reads in the regions, and thus the md5s
-- GenomeAnalysisEngineUnitTest needs to provide non-null genome loc parser
Merge pull request #46 from broadinstitute/md_active_regions_GSA-770

ActivityProfile and ActiveRegions respects engine interval boundaries
Fix for calculating read pos rank sum test with reads that are informative but don't actually overlap the variant due to some hard clipping.

-- Updated a few integration tests for HC, UG, and UG general ploidy
Reduce memory footprint of SyntheticRead by replacing several Lists with a single List of a small private static
class that contains the attributes that were scattered across the several Lists.
Added verbose error message to the PluginManager

-- added a logger.error with a more descriptive message of what the most likely cause of the error is

Typical error happens when a walker's global variable is not initialized properly (usually in test conditions). The old error message was very hard to understand "Could not create module because of an exception of type NullPointerException ocurred caused by exception null"
Fixed IndelRealigner reference length bug (GSA-774)

-- modified ReadBin GenomeLoc to keep track of softStart() and softEnd() of the reads coming in, to make sure the reference will always be sufficient even if we want to use the soft-clipped bases
-- changed the verification from readLength to aligned bases to allow reads with soft-clipped bases
-- switched TreeSet -> PriorityQueue in the ConstrainedMateFixer as some different reads can be considered equal by picard's SAMRecordCoordinateComparator (the Set was replacing them)
-- pulled out ReadBin class so it can be testable
-- added unit tests for ReadBin with soft-clips
-- added tests for getMismatchCount (AlignmentUtils) to make sure it works with soft-clipped reads

GSA-774 #resolve
Added GATKDocs fct to indicate default Read Filters for each tool

-- Added getClazzAnnotations() as hub to retrieve various annotations values and class properties through reflection
-- Added getReadFilters() method to retrieve Read Filter annotations
-- getReadFilters() uses recursion to walk up the inheritance to also capture superclass annotations
-- getClazzAnnotations() stores collected info in doc handler root, which is unit.forTemplate in Doclet
-- Modified FreeMarker template to use the Readfilters info (displayed after arg table, before additional capabilities)
-- Tadaaa :-) #GSATDG-63 resolve
Merge pull request #48 from broadinstitute/rp_calcAlignmentByteArrayOffset_contract_GSA-772

Fix for calculating read pos rank sum test with reads that are informati...
Hide arguments related to reference sample operation in UG - for internal use only until paper is published and docs are polished.
Merge pull request #45 from broadinstitute/mc_fix_indelrealigner_GSA-774

Fix to the Indel Realigner bug described in GSA-774
Merge pull request #49 from broadinstitute/gda_hidden_ug_args

Hide arguments related to reference sample operation in UG - for interna...
Extend timeout of NanoScheduler deadlock tests

-- The previous timeout of 1 second was just dangerously short.  Increase the timeout to 10 seconds
Merge pull request #40 from broadinstitute/gg_retrieve_readfilters_GSATDG-63
Added new ReadFilter that allows users to specifically reassign one single mapping quality to a different value. Useful for TopHat and other RNA-seq software users.
Merge pull request #47 from broadinstitute/aw_reduceread_perf_1_GSA-761

Reduce memory footprint of SyntheticRead by replacing several Lists with...
Merge pull request #50 from broadinstitute/gg_new_ReassignOneMappingQualityFilter_GSATDG-77

New ReadFilter allows users to reassign a specific mapping quality...
Added several more info types / annotations to GATKDocs
-- top-level walker type (locus, read etc)
-- parallelism options (nt or nct)
-- annotation type (for Variant Annotations)
-- downsampling settings that override engine defaults
-- reference window size
-- active region settings
-- partitionBy info