.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH FASTAQ_INSERT_OR_DELETE_BASES "1" "October 2014" "Fastaq" "Fastaq executables"
.SH NAME
fastaq_insert_or_delete_bases
.SH DESCRIPTION
 fastaq_insert_or_delete_bases <fasta/q in> <outfile>
.PP
Deletes or inserts bases at given position(s) from a fasta/q file
.SS "positional arguments:"
.TP
infile
Name of fasta/q file to be read
.TP
outfile
Name of output file
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-d\fR Name:start:bases, \fB\-\-delete\fR Name:start:bases
Delete the given bases from the given sequence. Format
same as samtools view: name:start\-end. This option can
be used multiple times (once for each region to
delete). Overlapping coords will be merged before
deleting
.TP
\fB\-\-delete_range\fR P,start,step
Deletes bases starting at position P in each sequence
of the input file. Deletes start + (n\-1)*step bases
from sequence n.
.TP
\fB\-i\fR Name:start:bases, \fB\-\-insert\fR Name:start:bases
Insert a random string of bases at the given position.
Format is name:position:number_to_add. Bases are added
after the position. This option can be used multiple
times
.TP
\fB\-\-insert_range\fR P,start,step
Inserts random bases starting after position P in each
sequence of the input file. Inserts start + (n\-1)*step
bases into sequence n.


.SH "AUTHOR"
.sp
fastaq_insert_or_delete_bases was originally written by Martin Hunt (mh12@sanger.ac.uk)

.SH "COPYING"
.sp
Wellcome Trust Sanger Institute Copyright \(co 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version\&.