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overlapInCore
~~~~~~
::
* No kmer length supplied; -k needed!
ERROR: No output file name specified
USAGE: overlapInCore [options] <gkpStorePath>
-b <fn> in contig mode, specify the output file
-c contig mode. Use 2 frag stores. First is
for reads; second is for contigs
-G do partial overlaps
-h <range> to specify fragments to put in hash table
Implies LSF mode (no changes to frag store)
-I designate a file of frag iids to limit olaps to
(Contig mode only)
-k if one or two digits, the length of a kmer, otherwise
the filename containing a list of kmers to ignore in
the hash table
-l specify the maximum number of overlaps per
fragment-end per batch of fragments.
-m allow multiple overlaps per oriented fragment pair
-M specify memory size. Valid values are '8GB', '4GB',
'2GB', '1GB', '256MB'. (Not for Contig mode)
-o specify output file name
-P write protoIO output (if not -G)
-r <range> specify old fragments to overlap
-t <n> use <n> parallel threads
-u allow only 1 overlap per oriented fragment pair
-w filter out overlaps with too many errors in a window
-z skip the hopeless check
--maxrate <n> only output overlaps with fraction <n> or less error (e.g., 0.06 == 6%)
--minlength <n> only output overlaps of <n> or more bases
--hashbits n Use n bits for the hash mask.
--hashstrings n Load at most n strings into the hash table at one time.
--hashdatalen n Load at most n bytes into the hash table at one time.
--hashload f Load to at most 0.0 < f < 1.0 capacity (default 0.7).
--maxreadlen n For batches with all short reads, pack bits differently to
process more reads per batch.
all reads must be shorter than n
--hashstrings limited to 2^(30-m)
Common values:
maxreadlen 2048->hashstrings 524288 (default)
maxreadlen 512->hashstrings 2097152
maxreadlen 128->hashstrings 8388608
--readsperbatch n Force batch size to n.
--readsperthread n Force each thread to process n reads.
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