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splitReads
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usage: splitReads -G gkpStore -O ovlStore -Ci input.clearFile -Co output.clearFile -o outputPrefix]
-G gkpStore path to read store
-O ovlStore path to overlap store
-o name output prefix, for logging
-t bgn-end limit processing to only reads from bgn to end (inclusive)
-Ci clearFile path to input clear ranges (NOT SUPPORTED)
-Co clearFile path to output clear ranges
-e erate ignore overlaps with more than 'erate' percent error
-minlength l reads trimmed below this many bases are deleted
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