gt-encseq-encode1
Encode sequence files (fasta/fastq, genbank, embl) efficiently.
Usage
gt encseq
encode
sequence_file
[sequence_file
[sequence_file ...]]
Overview
-
-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)
-
-dust [yes|no] -
mask low-complexity regions using the dust algorithm (default: no)
-
-dustwindow [value] -
windowsize for the dust algorithm (default: 64)
-
-dustthreshold [value] -
threshold for the dust algorithm (default: 2.000000)
-
-dustlink [value] -
Max. distance between regions masked by dust before merging. (default: 1)
-
-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
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.
-dust since Debian 12 (Bookworm);
-dustlink since Debian 12 (Bookworm);
-dustthreshold since Debian 12 (Bookworm);
-dustwindow since Debian 12 (Bookworm).