Tests are more rigorous and includes many more test cases.
We can tests custom cigars and the generated cigars.
*Still needs debugging because code is not working.
Created test classes to be used across several tests.
Some cases are still commented out.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Insertions are a problem so cigar cases with "I" are commented out.
The test works with multiple deletions and matches.
This is still not a complete test. A lot of cigar test cases are commented out.
Added insertions to ReadClipperUnitTest
ReadClipper now tests for all indels.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
The GATK engine will now provide a GATKSAMRecord to all tools which incorporates the functionality used by the GATK to the bam file (ReadGroups, Reduced Reads, ...).
* No tools should create SAMRecord anymore, use GATKSAMRecord instead *
* Includes tests that include HardClip to Read and Reference Coords.
* Changed ReadUtils.HardClipByReferenceCoordinates from private to protected to allow for testing
Mauricio Carneiro
Roger Zurawicki