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@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
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