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
Fix typo in method name: readRunfoder