NAME

       gt-tagerator - Map short sequence tags in given index.

SYNOPSIS

       gt tagerator [options] -q tagfile [-esa|-pck] indexname

OPTIONS

       -q
           Specify files containing the short sequence tags

       -e
           Specify the allowed number of differences (replacements/insertions/deletions)
           (default: -1)

       -esa
           Specify index (enhanced suffix array) (default: undefined)

       -pck
           Specify index (packed index) (default: undefined)

       -nod
           Do not compute direct matches (default: no)

       -nop
           Do not compute palindromic matches (i.e. no reverse complemented matches.) (default:
           no)

       -best
           Compute only best matches, i.e. only for smallest edit distance with matches (default:
           no)

       -maxocc
           specify max number of match-occurrences (default: 0)

       -skpp
           Skip prefix of pattern (only in pdiff mode) (default: no)

       -withwildcards
           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
           be verbose (default: no)

       -help
           display help and exit

       -version
           display version information and exit

AUTHOR

       Report bugs to <kurtz@zbh.uni-hamburg.de>.

                                            10/07/2012                            GT-TAGERATOR(1)