Fix issue 283 hardclips Index out of range error #293
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PolinaBevad
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PolinaBevad
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Description
This PR fixes issue when we have H base after Indels (#283).
The reason of the error is that we are trying to create complex variant from Indel and next H base (and we don't have a quality or sequence for hard clips).
Now it will check if we have
Hafter Indel and do not run complex adjusting then (variants will be stay as is).Test case is added. As Hard-clips aren't included in length of read, we have to use
-P 0option if variants near ends before H are needed.