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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
@CO Starting with I isn't handled due to the pileup ordering.
@CO The record only appears in the pileup list when the first base
@CO is placed against the reference, which is too late.
@CO
@CO 1
@CO 1234 56789 0123 Depadded base numbering
@CO ref TAGC TTAGC AGGT
@CO sD1 TAGCAA*****TTAGGT 4M 2I 5D 2I 4M
@CO sD2 TAGCA*******TAGGT 4M 1I 1P 5D 1P 1I 4M
@CO sD3 TAGC*A*****T*AGGT 4M 1P 1II 5D 1I 1P 4M
@CO sN1 TAGCAA>>>>>TTAGGT 4M 2I 5N 2I 4M
@CO sN2 TAGCA*>>>>>*TAGGT 4M 1I 1P 5N 1P 1I 4M
@CO sN3 TAGC*A>>>>>T*AGGT 4M 1P 1I 5N 1I 1P 4M
@CO qual ABCDEF GHIJKL
@CO
sD1 0 z 1 0 4M2I5D2I4M * 0 0 TAGCAATTAGGT ABCDEFGHIJKL
sD2 0 z 1 0 4M1I1P5D1P1I4M * 0 0 TAGCATAGGT ABCDEHIJKL
sD3 0 z 1 0 4M1P1I5D1I1P4M * 0 0 TAGCATAGGT ABCDFGIJKL
sN1 0 z 1 0 4M2I5N2I4M * 0 0 TAGCAATTAGGT ABCDEFGHIJKL
sN2 0 z 1 0 4M1I1P5N1P1I4M * 0 0 TAGCATAGGT ABCDEHIJKL
sN3 0 z 1 0 4M1P1I5N1I1P4M * 0 0 TAGCATAGGT ABCDFGIJKL
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