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vcf-file-1 VCF file (can be gzipped or bgzipped)
vcf-file-1 VCF file (can be gzipped or bgzipped)
vcf-file-2 VCF file (can be gzipped or bgzipped)
vcf-file-2 VCF file (can be gzipped or bgzipped)
genome-file Memory Mapped Sequence file
genome-file Memory Mapped Sequence file
(note that if genome.fa is specified, the actual file looked for is genome-bs.umfa)
w window size to detect overlaps between variants
w window size to detect overlaps between variants
d debug option to generate a match.log file that gives all the matches made
d debug option to generate a match.log file that gives all the matches made
