Update the NM and MD tags when clipping overlapping inserts in #622
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MergeBamAlignment.
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@bradtaylor any chance you could review this today? I am blocked by this bug. |
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Looked at this just now. LGTM. 👍 |
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Thank-you @yfarjoun! |
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1. Rename SetNmAndUqTags to SetNmMDAndUqTags. WIP 2. Fixes: #622
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1. Rename SetNmAndUqTags to SetNmMDAndUqTags. WIP 2. Fixes: #622
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Aug 20, 2016
1. Rename SetNmAndUqTags to SetNmMDAndUqTags. WIP 2. Fixes: #622
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Aug 26, 2016
1. Rename SetNmAndUqTags to SetNmMDAndUqTags. WIP 2. Fixes: #622
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1. Rename SetNmAndUqTags to SetNmMDAndUqTags. WIP 2. Fixes: #622
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1. Rename SetNmAndUqTags to SetNmMDAndUqTags. 2. Fixes: #622
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1. Rename SetNmAndUqTags to SetNmMDAndUqTags. 2. Fixes: #622
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MergeBamAlignment.
The bug comes from changing the cigar but not updating the NM and MD tags.
I modified the clipping test to check the MD and NM tags for FR reads. The MD and NM tags for the clipped versus not-clipped should be "76" vs. "56" (MD) and from "1" vs. "0" (NM). For the latter, I inserted a mismatch into the clipped bases for the clipped reads.
@yfarjoun or @ktibbett would you care to review (git blame tells me @ktibbett last touched this in 2011!)?