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aligner core: annotated-junction stitching, alignEndsType, in-recursion length penalty - #146

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aligner core: annotated-junction stitching, alignEndsType, in-recursion length penalty#146
BenjaminDEMAILLE wants to merge 17 commits into
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BenjaminDEMAILLE:bd/aligner-core-faithfulness

docs(divergence): trace the remaining PE pair to the seed search

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