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ovStoreDump
~~~~~~
::
usage: ovStoreDump -G gkpStore -O ovlStore ...
There are three modes of operation:
-d [a[-b]] dump overlaps for reads a to b, inclusive
-q a b report the a,b overlap, if it exists.
-p a dump a picture of overlaps to fragment 'a'.
FORMAT (for -d)
-coords dump overlap showing coordinates in the reads (default)
-hangs dump overlap showing dovetail hangs unaligned
-raw dump overlap showing its raw native format (four hangs)
-paf dump overlaps in miniasm/minimap format
-binary dump overlap as raw binary data
-counts dump the number of overlaps per read
MODIFIERS (for -d and -p)
-E erate Dump only overlaps <= erate fraction error.
-L length Dump only overlaps that are larger than L bases (only for -p picture mode).
-d5 Dump only overlaps off the 5' end of the A frag.
-d3 Dump only overlaps off the 3' end of the A frag.
-dC Dump only overlaps that are contained in the A frag (B contained in A).
-dc Dump only overlaps that are containing the A frag (A contained in B).
-v Report statistics (to stderr) on some dumps (-d).
-unique Report only overlaps where A id is < B id, do not report both A to B and B to A overlap
-best prefix Annotate picture with status from bogart outputs prefix.edges, prefix.singletons, prefix.edges.suspicious
-noc With -best data, don't show overlaps to contained reads.
-nos With -best data, don't show overlaps to suspicious reads.
ERROR: no operation (-d, -q or -p) supplied.
ERROR: no input gkpStore (-G) supplied.
ERROR: no input ovlStore (-O) supplied.
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