GT-PACKEDINDEX-MKI(1)

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>.