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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 1 2345 6789012 3 Depadded base numbering
@CO ref T AGCT TAGCAGG T
@CO
@CO s1 AGCT TAGCAGG 11M
@CO s2 AGCTCCCTAGCAGG 4M 3I 7M
@CO s3 A=AGCT TAGCAGG=A 2I 11M 2I
@CO AB0123ABC4567890CD
@CO
s1 0 z 2 0 11M * 0 0 AGCTTAGCAGG 01234567890
s2 0 z 2 0 4M3I7M * 0 0 AGCTCCCTAGCAGG 0123ABC4567890
s2 0 z 2 0 2I11M2I * 0 0 A=AGCTTAGCAGG=A AB01234567890CD
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