2be5704a25
haplotypes were being clipped to the reference window when their unclipped ends went beyond the reference window. The unclipped ends include the hard clipped bases, therefore, if the reference window ended inside the hard clipped bases of a read, the boundaries would be wrong (and the read clipper was throwing an exception). * updated code to use SoftEnd/SoftStart instead of UnclippedEnd/UnclippedStart where appropriate. * removed unnecessary code to remove hard clips after processing. * reorganized the logic to use the assigned read boundaries throughout the code (allowing it to be final). |
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