Currently, we hard-code the assumption that vcf files will have a tabix (.tbi) index, but pysam can use either a .csi or a .tbi index. In order to allow either index style, we need to check for presence of each file and only throw a file does not exist warning if neither index exists.
tsackton
commented
1 year ago
Currently, we hard-code the assumption that vcf files will have a tabix (.tbi) index, but pysam can use either a .csi or a .tbi index. In order to allow either index style, we need to check for presence of each file and only throw a file does not exist warning if neither index exists.