NEW: add report to extract-reads enabling interrogation of why reads were/were not extracted#222
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gregcaporaso wants to merge 5 commits intoqiime2:devfrom
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NEW: add report to extract-reads enabling interrogation of why reads were/were not extracted#222gregcaporaso wants to merge 5 commits intoqiime2:devfrom
gregcaporaso wants to merge 5 commits intoqiime2:devfrom
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Adds a second output `read_extraction_stats` (ImmutableMetadata) to the `extract_reads` action. The new artifact is a per-input-sequence TSV reporting: extraction outcome, match orientation and method (exact vs approximate), forward/reverse primer binding positions in the matched-orientation sequence, per-primer match percentages, amplicon length before and after trimming, and input sequence length. Adds two unit tests asserting that _gen_reads returns the same amplicon when given a sequence and its reverse complement (read_orientation='both'), covering both the exact-match and approximate-match code paths and asserting the expected match-method and match-orientation stats. Updated internal helpers: `_align_primer` now returns a named tuple with primer binding coordinates; `_exact_match` and `_approx_match` return richer result tuples. `_gen_reads` always returns a (amplicon, stats) pair. Note from @gregcaporaso: Claude was used in the development of the code and the tests. I did a full review of the code and tests before passing this along for code review by another human. Claude's tests were a bit underwhelming - that is where I made most of my modifications. For example, all values in test_extract_reads_stats_all_extracted were hand-calculated by me (Claude previously had very general tests of the output stats). This is my first use of Claude for new functionality going into a QIIME 2 plugin. The new output table has already been very helpful for me in a few exploratory analyses that I've run, and I next hope to use this to validate that some code simplifications that I want to make in extract_reads don't impact the results in ways that I don't want them to (this was very hard to assess in my previous recent work on this action). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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colinvwood
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May 5, 2026
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Replacing #221.