.TH NORMALISEFASTA 1 "January 2014" BIOBAMBAM
.SH NAME
normalisefasta - normalise line length in a FastA file
.SH SYNOPSIS
.PP
.B normalisefasta
[options]
.SH 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.
.PP
The following key=value pairs can be given:
.PP
.B 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)
.PP
.B bgzf=<0|1>
produce uncompressed (bgzf=0) or compressed (bgzf=1) output
.PP
.B 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.
.PP
.B level=<-1|0|1|9|11>:
set compression level of the output file if bgzf=1. Valid
values are
.IP -1:
zlib/gzip default compression level
.IP 0:
uncompressed
.IP 1:
zlib/gzip level 1 (fast) compression
.IP 9:
zlib/gzip level 9 (best) compression
.P
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
.IP 11:
igzip compression
.PP
.B minlength=<[0]>
Minimum length. Reads shorter than this will be discarded. By default all
reads are kept.
.SH AUTHOR
Written by German Tischler.
.SH "REPORTING BUGS"
Report bugs to <germant@miltenyibiotec.de>
.SH COPYRIGHT
Copyright \(co 2009-2014 German Tischler, \(co 2011-2014 Genome Research Limited.
License GPLv3+: GNU GPL version 3 <http://gnu.org/licenses/gpl.html>
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.