Fix incorrect crash with "ERROR: sequence <name> was not found in the query file." #112
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If a contig is mapped to multiple reference chromosomes, then we need to store its sequence in each version of the contig.
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Fixes #105 |
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Only the last patch in this series is really needed.
When loading query sequences, it was not correct the break out of the loop on the first contig with the right name. The contig could occur multiple times in the list, possibly with different +/- directions. We need to copy the data for each instance.