Make calmd run faster on non-position-sorted data #1723
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Add caching so that calmd doesn't continuously have to reread reference sequences if the input does not go through them sequentially. As caching requires extra memory, it is only enabled if calmd detects an attempt to go backwards in the reference dictionary. Thus processing a position-sorted file uses no more space than before, while processing other orderings is now much faster.
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Adds caching so that calmd doesn't continuously have to reread reference sequences if the input does not go through them sequentially. As caching requires extra memory, it is only enabled if calmd detects an attempt to go backwards in the reference dictionary. Thus processing a position-sorted file uses no more space than before, while processing other orderings is now much faster.
Fixes #1595