feat: add HN tag to bwa aln #438
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This was referenced Jan 17, 2025
nh13
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This requires us to patch bwa, which we store in the patches sub-directory. They are applied before we build, and reverted after the build completes (regardless of success). They can be removed when the bwa PRs are merged and submodule updated. See: lh3/bwa#438 See: lh3/bwa#439
nh13
added a commit
to fulcrumgenomics/pybwa
that referenced
this pull request
Jan 17, 2025
This requires us to patch bwa, which we store in the patches sub-directory. They are applied before we build, and reverted after the build completes (regardless of success). They can be removed when the bwa PRs are merged and submodule updated. See: lh3/bwa#438 See: lh3/bwa#439
nh13
added a commit
to fulcrumgenomics/pybwa
that referenced
this pull request
Jan 17, 2025
This requires us to patch bwa, which we store in the patches sub-directory. They are applied before we build, and reverted after the build completes (regardless of success). They can be removed when the bwa PRs are merged and submodule updated. See: lh3/bwa#438 See: lh3/bwa#439
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Use the X0 and X1 tags |
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@lh3 would you be willing to reconsider this? The HN tag is a standard tag across aligners, while X0 and X1 are not, and so we need to translate from the latter two tags to the former, and this PR would remove that. The MD to the XA tag would be incredibly useful, especially when looking at the alignments of alternative hits, even if we don't want all of them. And then this would be analogous to the SA tag. What's the harm in adding both? |
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This is really useful when we want to know the # of hits found, not just the # reported (in the XA tag), which can be zero there were too many.