Add an option to cgw. It would generate extra output when an alignment
fails, leading to a negative gap between contigs. The report would list the
elements (reads, contigs) that failed to align.
Better than generating a report would be to avoid the problem, so I have renamed this case. The goal is never to output a negative gap inside a scaffold. There is code that tests whether contigs align, and those alignments should be allowed to fail. But the code that settles on an alignment should force the sequence to align or break the scaffold.
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Better than generating a report would be to avoid the problem, so I have renamed this case. The goal is never to output a negative gap inside a scaffold. There is code that tests whether contigs align, and those alignments should be allowed to fail. But the code that settles on an alignment should force the sequence to align or break the scaffold.