Merge Haploflow into master #1015
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…ches into pieces on the coverage map
…genome consensus for result
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Note that I am using a specific commit version for pinning. Rationalization: Haploflow is not developed actively, and because of that, the last release is quite far behind master. Thus, I think it's better to pin its version to the current master than to the latest release tag.
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This change does not handle `merged_contigs_csv`.
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