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 <germant@miltenyibiotec.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.