Merge pull request #53 from dkj/devel

Add appropriate PG field to RG header records
Test data from recent paired end HiSeq and associated test for xahuman
split with default parameters.
Add Truth table to unit test.
Test added for inverted file names;  INVERT_TARGET simple logic and
test.
Run test data through picard-tools-1.72/FixMateInformation after hand
editing: note that the * Y and Y * cases are changed to Y Y, but flags
remain correct for unaligned.  20 Y and Y 20 are not changed by
FixMateInformation.
Experiments with a different approach to INVERT_TARGET, tests passing.
Tests for EXCLUDE_UNALIGNED set to true for xahuman data (failing) and 
the reversed filenames for yhuman (failing) for historical reference.
Minimal change to existing logic for INVERT_TARGET
Use built-in XOR operator.
Make the default value of INVERT_TARGET to be false to protect future
uses.
Add failing test for xahuman with EXCLUDE_UNALIGNED set to true
Correct the first two truth tables in comments for the [Y|MT] 20 case:
functionality unchanged.
Correct MD5 values
Merge pull request #55 from KateTaylor/devel

SplitBamByChromosome new functionality for Y split
New test and proposed fix for EXCLUDE_UNALIGNED = true and default
S=Y,MT
Update versions ready for release
By-pass pull request #55
Merge pull request #56 from KateTaylor/devel

Release y_chromosome_split
Merge pull request #57 from wtsi-npg/devel

[Hinxton #354882] separate_y_chromosome_data
Add #52, #53, #55 to Changes
Merge pull request #58 from KateTaylor/devel

Add #52, #53, #55 to Changes. Y chromosome split is done via a new V flag to SplitBamByChromosomes to allow the target and excluded files to be inverted with some modifications to behaviour.