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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 123 45678 90123 Depadded base numbering
@CO ref TAG CTTAG CAGGT
@CO
@CO s1 AG CTTAGTT**GGC 7M 2I 2D 3M
@CO s2 AG CTTAGTT** 7M 2I 2D
@CO s3 AG CTTAGT*** 7M 1I 1P 2D
@CO s4 AA**TAG CAGG 2I 2D 7M
@CO s5 *A**TAG CAGG 1P 1I 2D 7M
@CO qual 01AB23456CD78901
@CO
s1 0 z 2 0 7M2I2D3M * 0 0 AGCTTAGTTGGC 0123456CD901
s2 0 z 2 0 7M2I2D * 0 0 AGCTTAGTT 0123456CD
s3 0 z 2 0 7M1I1P2D * 0 0 AGCTTAGT 0123456D
s4 0 z 4 0 2I2D7M * 0 0 AATAGCAGG AB4567890
s5 0 z 4 0 1P1I2D7M * 0 0 ATAGCAGG B4567890
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