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>.

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