GT-PACKEDINDEX-CHK(1)

NAME
gt-packedindex-chksearch - Load (or build if necessary) BWT index for project [indexname] and perform verification of search results.

SYNOPSIS

gt packedindex chksearch indexname

OPTIONS

-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)

-minpatlen
    minimum length of patterns searched for, -1 implies automatic choice based on index properties (default: -1)

-maxpatlen
    maximum length of patterns searched for, -1 implies automatic choice based on index properties (default: -1)

-nsamples
    number of sequences to search for (default: 1000)

-chksfxarray
    verify integrity of stored suffix array positions (default: no)

-full-lfmap
    verify complete backwards regeneration of original sequence (default: no)

-chkcontext
    verify integrity of regenerated sequence context (default: no)

-ticks
    print dot after this many symbols tested okay (default: 100000)

-v
    print verbose progress information (default: no)

-help
    display help and exit

-version
    display version information and exit

AUTHOR

Report bugs to <gt-users@genometools.org>.