@HD	VN:1.6	SO:coordinate
@SQ	SN:z	LN:13
@CO	
@CO	Copyright (c) 2018 Genome Research Ltd.
@CO	
@CO	Permission is hereby granted, free of charge, to any person obtaining
@CO	a copy of this software and associated documentation files (the
@CO	"Software"), to deal in the Software without restriction, including
@CO	without limitation the rights to use, copy, modify, merge, publish,
@CO	distribute, sublicense, and/or sell copies of the Software, and to
@CO	permit persons to whom the Software is furnished to do so, subject
@CO	to the following conditions:
@CO	
@CO	The above copyright notice and this permission notice shall be included
@CO	in all copies or substantial portions of the Software.
@CO	
@CO	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
@CO	OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
@CO	MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
@CO	IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
@CO	CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
@CO	TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
@CO	SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
@CO	
@CO	Various I combinations with (P)ads
@CO	
@CO	                  1
@CO	     12345    67890  Depadded base numbering
@CO	ref  AGCTT    AGCAG
@CO	
@CO	s1   AGCTT    AGCAG  10M
@CO	s2   AGCTTGGCCAGCAG  5M 4I 5M
@CO	s3   AGCTTGG**AGCAG  5M 2I 2P 5M
@CO	s4   AGCTT*GC*AGCAG  5M 1P 2I 1P 5M
@CO	s5   AGCTT**CCAGCAG  5M 2P 2I 5M
@CO	qual 01234ABCD56789
s1	0	z	2	0	10M	*	0	0	AGCTTAGCAG	0123456789
s2	0	z	2	0	5M4I5M	*	0	0	AGCTTGGCCAGCAG	01234ABCD56789
s3	0	z	2	0	5M2I2P5M	*	0	0	AGCTTGGAGCAG	01234AB56789
s4	0	z	2	0	5M1P2I1P5M	*	0	0	AGCTTGCAGCAG	01234BC56789
s5	0	z	2	0	5M2P2I5M	*	0	0	AGCTTCCAGCAG	01234CD56789
