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What's going on in src/SamSegmentMapper.cpp:226 #13

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vinjana opened this issue Jan 23, 2024 · 1 comment
Open

What's going on in src/SamSegmentMapper.cpp:226 #13

vinjana opened this issue Jan 23, 2024 · 1 comment
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@vinjana
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vinjana commented Jan 23, 2024

In src/SamSegmentMapper.cpp:226 it says

            if (!chrConverter.isTechnical(alignment.getMateChrIndex()) &&
                !(alignment.getMateChrIndex() == 2 &&
                  (alignment.getMatePos() / 10000 == 3314))) {

This seems like special code for hg37 ... 🤔

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vinjana commented Mar 19, 2024

Added isInIgnoredRegion to ChrConverter.

@vinjana vinjana self-assigned this Mar 19, 2024
@vinjana vinjana mentioned this issue Mar 19, 2024
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