-q
Specify files containing the short sequence tags
-e [value]
Specify the allowed number of differences (replacements/insertions/deletions)
-esa [string]
Specify index (enhanced suffix array) (default: undefined)
-pck [string]
Specify index (packed index) (default: undefined)
-nod [yes|no]
Do not compute direct matches (default: no)
-nop [yes|no]
Do not compute palindromic matches (i.e. no reverse complemented matches.) (default: no)
-best [yes|no]
Compute only best matches, i.e. only for smallest edit distance with matches (default: no)
-maxocc [value]
specify max number of match-occurrences (default: 0)
-skpp [yes|no]
Skip prefix of pattern (only in pdiff mode) (default: no)
-withwildcards [yes|no]
output matches containing wildcard characters (e.g. N); only relevant for approximate matching
(default: yes)
-output
use combination of the following keywords to specify output tagnum show ordinal number of tag tagseq
show tag sequence dblength show length of match in database dbstartpos show start position of match
in database abspos show absolute value of dbstartpos dbsequence show sequence of match strand show
strand edist show edit distance tagstartpos show start position of match in tag (only for -maxocc)
taglength show length of match in tag (only for -maxocc) tagsuffixseq show suffix tag involved in
match (only for -maxocc)
-v [yes|no]
be verbose (default: no)
-help
display help and exit
-version
display version information and exit
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