Seems to produce correct bam files for secondary and supplementary alignments.
Just the metrics to correct now...
Metrics now work for regression tests
Remove debug code
Name change
Merge remote-tracking branch 'js10-remote/devel' into devel
Peekable iterator implements SAMRecordIterator

and so avoid need for extra class (at expense of adding a few methods)
Inner utility iterator class (can and should be) made static
make method static if it does not use object data or methods
Merge pull request #1 from dkj/devel

Alternative inner class, use of static.
Do not use bit mask to test flags
Exception if template alignment records are out of order

AlignmentFilter should take records (for same primary data) from
multiple BAM files - if template groups f reocrds or out of order
compared with the first file, or missing form the first file then
an exception should be thrown.
Fix unchecked conversion javac lint warning for ArrayList
Merge pull request #2 from dkj/devel

Explode if templates are out of order
Added unit test for supplementary reads
Make sure seperate tests write to seperate subdirectories
metric.checkNextReadsForChimera now working properly
Added test data and unit tests for chimeric reads
Merge pull request #67 from jenniferliddle/devel

Handle secondary alignments