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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 1234567890123 Depadded base numbering
@CO ref TAGCTTAGCAGGT
@CO s1 AGCTTAGCAGG 11M
@CO s2 AGCT>>>CAGG 4M 3N 4M
@CO s3 >>CTTAGCA>> 2N 7M 2N
@CO qual 01234567890
@CO
s1 0 z 2 0 11M * 0 0 AGCTTAGCAGG 01234567890
s2 0 z 2 0 4M3N4M * 0 0 AGCTCAGG 01237890
s3 0 z 2 0 2N7M2N * 0 0 CTTAGCA 2345678
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