'\" t
.\" Title: gt-repfind
.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author]
.\" Generator: DocBook XSL Stylesheets v1.79.1
.\" Date: 10/28/2018
.\" Manual: GenomeTools Manual
.\" Source: GenomeTools 1.5.10
.\" Language: English
.\"
.TH "GT\-REPFIND" "1" "10/28/2018" "GenomeTools 1\&.5\&.10" "GenomeTools Manual"
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.SH "NAME"
gt-repfind \- Compute maximal exact matches (and more)\&.
.SH "SYNOPSIS"
.sp
\fBgt repfind\fR [options] \-ii indexname
.SH "DESCRIPTION"
.PP
\fB\-l\fR [\fIvalue\fR]
.RS 4
Specify minimum length of matches (default: 0)
.RE
.PP
\fB\-f\fR [\fIyes|no\fR]
.RS 4
Compute forward matches (default: yes)
.RE
.PP
\fB\-r\fR [\fIyes|no\fR]
.RS 4
Compute reverse matches (default: no)
.RE
.PP
\fB\-p\fR [\fIyes|no\fR]
.RS 4
Compute matches on reverse strand (default: no)
.RE
.PP
\fB\-seedlength\fR [\fIvalue\fR]
.RS 4
Specify minimum length of seed (default: 0)
.RE
.PP
\fB\-maxfreq\fR [\fIvalue\fR]
.RS 4
Specify maximal frequency of maximal exact matches in reference sequence (default: 0)
.RE
.PP
\fB\-extendxdrop\fR [\fIvalue\fR]
.RS 4
Extend seed to both sides using xdrop algorithm, optional parameter specifies sensitivity (default: 97)
.RE
.PP
\fB\-xdropbelow\fR [\fIvalue\fR]
.RS 4
Specify xdrop cutoff score (argument 0 means undefined)\&. If undefined an optimal value is determined automatically depending on the error rate
.RE
.PP
\fB\-extendgreedy\fR [\fIvalue\fR]
.RS 4
Extend seed to both sides using greedy algorithm with trimming of waves, optional parameter specifies sensitivity (default: 97)
.RE
.PP
\fB\-minidentity\fR [\fIvalue\fR]
.RS 4
Specify minimum identity of matches as integer in the range from 70 to 99 (for xdrop and greedy extension) (default: 80)
.RE
.PP
\fB\-ii\fR [\fIstring\fR]
.RS 4
Specify input index (default: undefined)
.RE
.PP
\fB\-outfmt\fR
.RS 4
specify what information about the matches to display alignment: show alignment (possibly followed by = to specify width of alignment columns, default is ) seed_in_algn: mark the seed in alignment polinfo: add polishing information for shown alignment seed: abbreviation for seed\&.len seed\&.s seed\&.q failed_seed: show the coordinates of a seed extension, which does not satisfy the filter conditions fstperquery: output only the first found match per query tabsep: separate columns by tabulator, instead of space as default blast: output matches in blast format 7 (tabular with comment lines; instead of gap opens, indels are displayed) gfa2: output matches in gfa2 format custom: output matches in custom format, i\&.e\&. no columns are pre\-defined; all columns have to be specified by the user cigar: display cigar string representing alignment (no distinction between match and mismatch) cigarX: display cigar string representing alignment (distinction between match (=) and mismatch (X)) trace: display trace, i\&.e\&. a compact representation of an alignment (possibly followed by =) to specify the delta\-value; default value of delta is 50 dtrace: display trace as differences; like trace, but instead of an absolute value x, report the difference delta\-x\&. This leads to smaller numbers and thus a more compact representation s\&.len: display length of match on subject sequence s\&.seqnum: display sequence number of subject sequence subject id: display sequence description of subject sequence s\&.start: display start position of match on subject sequence s\&.end: display end position of match on subject sequence strand: display strand of match using symbols F (forward) and P (reverse complement) q\&.len: display length of match on query sequence q\&.seqnum: display sequence number of query sequence query id: display sequence description of query sequence q\&.start: display start position of match on query sequence q\&.end: display end position of match on query sequence alignment length: display length of alignment mismatches: display number of mismatches in alignment indels: display number of indels in alignment gap opens: display number of indels in alignment score: display score of match editdist: display unit edit distance identity: display percent identity of match seed\&.len: display length seed of the match seed\&.s: display start position of seed in subject seed\&.q: display start position of seed in query s\&.seqlen: display length of subject sequence in which match occurs q\&.seqlen: display length of query sequence in which match occurs evalue: display evalue bit score: display bit score
.RE
.PP
\fB\-evalue\fR [\fIvalue\fR]
.RS 4
switch on evalue filtering of matches (optional argument specifies evalue threshold) (default: 10\&.000000)
.RE
.PP
\fB\-scan\fR [\fIyes|no\fR]
.RS 4
scan index rather than map it to main memory (default: no)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to \&.