SAMFragment end position is wrong

[pamelarussell]

SAMFragment.getReferenceEndPosition() calculates the end position by adding the size to the start position. Size is the sum of the sizes of the blocks and does not include introns. Therefore the reference end position is wrong.

[charcuterie]

I have this changed in my branch. I never figured out what the "incorrect CIGAR parser" referred to in the comment. Returning the code to

return record.getAlignmentEnd()

works for me, and passes my unit tests.

[pamelarussell]

Has this been committed? I'm still getting the same bug.