NAME

       normalisefasta - normalise line length in a FastA file

SYNOPSIS

       normalisefasta [options]

DESCRIPTION

       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=<[80]> 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

       -1:    zlib/gzip default compression level

       0:     uncompressed

       1:     zlib/gzip level 1 (fast) compression

       9:     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

       11:    igzip compression

       minlength=<[0]>  Minimum length. Reads shorter than this will be discarded. By default all
       reads are kept.

AUTHOR

       Written by German Tischler.

REPORTING BUGS

       Report bugs to <tischler@mpi-cbg.de>

COPYRIGHT

       Copyright © 2009-2014 German Tischler,  ©  2011-2014  Genome  Research  Limited.   License
       GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
       This  is free software: you are free to change and redistribute it.  There is NO WARRANTY,
       to the extent permitted by law.