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Bug fix for something Guillermo added to UG before he left to support…
… calling indels from reduced reads. His code was excessively clipping reads because it was looking at their cigar string instead of just the read length. This meant that it was basically impossible to call large deletions in UG even with perfect evidence in the reads (as reported by Craig D). Integration tests change because (IMO after looking at sites in IGV) reads with indels similar to the one being genotyped used to be given too much likelihood and now give less. Added unit tests for new methods.
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