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GT-ENCSEQ-ENCODE(1) GenomeTools Manual GT-ENCSEQ-ENCODE(1)

NAME

gt-encseq-encode - Encode sequence files efficiently.

SYNOPSIS

gt encseq encode sequence_file [sequence_file [sequence_file ...]]

DESCRIPTION

-showstats [yes|no]
show compression results (default: no)
-ssp [yes|no]
output sequence separator positions to file (default: yes)
-des [yes|no]
output sequence descriptions to file (default: yes)
-sds [yes|no]
output sequence description separator positions to file (default: yes)
-md5 [yes|no]
output MD5 sums to file (default: yes)
-clipdesc [yes|no]
clip descriptions after first whitespace (default: no)
-sat [string]
specify kind of sequence representation by one of the keywords direct, bytecompress, eqlen, bit, uchar, ushort, uint32 (default: undefined)
-dna [yes|no]
input is DNA sequence (default: no)
-protein [yes|no]
input is protein sequence (default: no)
-plain [yes|no]
process as plain text (default: no)
-indexname [string]
specify name for index to be generated (default: undefined)
-smap [string]
specify file containing a symbol mapping (default: undefined)
-lossless [yes|no]
allow lossless original sequence retrieval (default: no)
-v [yes|no]
be verbose (default: no)
-help
display help for basic options and exit
-help+
display help for all options and exit
-version
display version information and exit

REPORTING BUGS

Report bugs to <gt-users@genometools.org>.
09/05/2014 GenomeTools 1.5.3