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trimReads
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::
usage: trimReads -G gkpStore -O ovlStore -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 ouput clear ranges
-e erate ignore overlaps with more than 'erate' percent error
-ol l the minimum evidence overlap length
-oc c the minimum evidence overlap coverage
evidence overlaps must overlap by 'l' bases to be joined, and
must be at least 'c' deep to be retained
-minlength l reads trimmed below this many bases are deleted
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