feat: Support custom contig sep characters in pairix index#398
Merged
nvictus merged 3 commits intoopen2c:masterfrom Mar 8, 2024
Merged
feat: Support custom contig sep characters in pairix index#398nvictus merged 3 commits intoopen2c:masterfrom
nvictus merged 3 commits intoopen2c:masterfrom
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GarrettNg
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Mar 8, 2024
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By default, the
|character is used to delimit contig names in pairix index blocks, e.g.chr1|chr1,chr1|chr2, etc.However, many FASTA sequence names contain pipes, which conflicts with this usage. Pairix supports creating an index with a different contig separator using
-w, but this hasn't been supported incooler cload pairix. See #234.This PR lets the user provide a custom separator to
cooler cload pairixvia--block-charif it happens to be known or is discovered by the user (unfortunately, pypairix provides no way to determine this character dynamically) and will error if the separator is incorrect.