|NORMALISEFASTA(1)||General Commands Manual||NORMALISEFASTA(1)|
normalisefasta - normalise line length in a FastA file
normalisefasta reads a FastA file from standard input and outputs a reformatted version of the file with a consistent length of the lines containing sequence information on standard output. The program can either produce uncompressed or BGZF compressed output. For uncompressed output a FastA index (.fai) is produced on the standard error channel.
The following key=value pairs can be given:
cols=<> line width for the lines containing sequence information in number of bases. This option is only considered for uncompressed output (i.e. bgzf=0)
bgzf=<0|1> produce uncompressed (bgzf=0) or compressed (bgzf=1) output
index=<> if bgzf=1 this key can be used for giving the file name for the index file allowing (pseudo) random access in the output file. If the key is not given when bgzf=1, then no index is written.
level=<-1|0|1|9|11>: set compression level of the output file if bgzf=1. Valid values are
- zlib/gzip default compression level
- zlib/gzip level 1 (fast) compression
- zlib/gzip level 9 (best) compression
If libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then an additional valid value is
- igzip compression
minlength=<> Minimum length. Reads shorter than this will be discarded. By default all reads are kept.
Written by German Tischler.
Report bugs to <email@example.com>
Copyright © 2009-2014 German Tischler, © 2011-2014
Genome Research Limited. License GPLv3+: GNU GPL version 3
This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.