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Add option for a custom alignment file in caprieval - #1418

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AnnaKravchenko wants to merge 11 commits into
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cust-alig-capri
Draft

Add option for a custom alignment file in caprieval#1418
AnnaKravchenko wants to merge 11 commits into
mainfrom
cust-alig-capri

rename alig_fname to align_fname v2

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