NAME

       gt-packedindex-mkindex - Compute packed index.

SYNOPSIS

       gt packedindex mkindex [option ...] (-db file [...] | -ii index)

OPTIONS

       -ssp
           output sequence separator positions to file (default: yes)

       -des
           output sequence descriptions to file (default: yes)

       -sds
           output sequence description separator positions to file (default: yes)

       -md5
           output MD5 sums to file (default: yes)

       -sat
           specify kind of sequence representation by one of the keywords direct, bytecompress,
           eqlen, bit, uchar, ushort, uint32 (default: undefined)

       -dna
           input is DNA sequence (default: no)

       -protein
           input is protein sequence (default: no)

       -indexname
           specify name for index to be generated (default: undefined)

       -db
           specify database files

       -smap
           specify file containing a symbol mapping (default: undefined)

       -lossless
           allow lossless original sequence retrieval (default: no)

       -mirrored
           virtually append the reverse complement of each sequence (default: no)

       -pl
           specify prefix length for bucket sort recommendation: use without argument; then a
           reasonable prefix length is automatically determined. (default: 0)

       -dc
           specify difference cover value (default: 0)

       -kys
           output/sort according to keys of the form |key| in fasta header (default: nosort)

       -dir
           specify reading direction (fwd, cpl, rev, rcl) (default: fwd)

       -bsize
           specify size of blocks (default: 8)

       -blbuck
           specify number of blocks per bucket (default: 8)

       -locfreq
           specify the locate frequency parameter i means that each i-th position of input string
           is stored 0 ⇒ no locate information (default: 16)

       -locbitmap
           marked/unmarked positions for locate are stored as bitmaps this gives faster location
           of hits but increases the index by 1 bit per symbol (default: yes)

       -sprank
           build rank table for special symbols this produces an index which can be used to
           regenerate the original sequence but increases the memory used during index creation
           (default: no)

       -sprankilog
           specify the interval of rank sampling as log value parameter i means that each 2^i-th
           position of source is sampled for rank undefined ⇒ chooses default of log(log(sequence
           length)) (default: undefined)

       -ctxilog
           specify the interval of context sampling as log value parameter i means that each
           2^i-th position of source is sampled for rank -1 ⇒ chooses default of log(log(sequence
           length)) -2 ⇒ generates no map (default: -2)

       -v
           be verbose (default: no)

       -showprogress
           show a progress bar (default: no)

       -ii
           specify existing encoded sequence (default: undefined)

       -help
           display help for basic options and exit

       -help+
           display help for all options and exit

       -version
           display version information and exit

AUTHOR

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

                                            10/07/2012                      GT-PACKEDINDEX-MKI(1)