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SAM/BAM alignment support #3

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esteinig opened this issue Mar 13, 2022 · 2 comments
Closed

SAM/BAM alignment support #3

esteinig opened this issue Mar 13, 2022 · 2 comments
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More general SAM/BAM format for alignment input
@esteinig esteinig added the new feature Documents a new feature for implementation label Mar 13, 2022
@esteinig esteinig self-assigned this Mar 13, 2022
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Leave for later releases as we are working with minimap2 for now

@esteinig esteinig added the later release Documents a feature for implementation in a later release label Mar 13, 2022
esteinig added a commit that referenced this issue Mar 15, 2022
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add extended outputs [#3]; start on coverage plot [#2]
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esteinig commented Mar 19, 2022 •
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I was running into a difference in reference alignment positions between standard PAF alignment output and the SAM output from minimap2. This appears due to not performing base-level alignment in the standard PAF output. Equivalence is:

minimap2 -a ref.fa reads.fq
minimap2 -c ref.fa reads.fq

but these are different

minimap2 -a ref.fa reads.fq
minimap2 ref.fa reads.fq

see also:

  • https://github.com/lh3/minimap2/issues/247
  • https://github.com/lh3/minimap2/issues/158

@esteinig esteinig removed the later release Documents a feature for implementation in a later release label Mar 20, 2022
@esteinig esteinig mentioned this issue Mar 23, 2022
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