Fix: -i and -d flags now respected in both classify modes (v2.7.1)#17
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Backport of the isoform-flag-parity fix from the v2.4.x maintenance line (v2.4.3) onto origin/main (v2.7.0). The in-memory post-extraction filter hardcoded longest_only=True and include_duplicates=False, ignoring CLI flags. The streaming per-contig worker hardcoded longest_only=True and did not have allow_multiple_isoforms plumbed into its config_dict. The extraction prefilter `should_extract_sequences_for` always skipped coord-duplicates regardless of include_duplicates. All three sites now consult config consistently; streaming/in-memory equivalence holds across all (-i, -d) flag combinations. Tests added: synthetic alt-isoform fixture (1 gene, 2 isoforms, 1 shared intron, 1 alt-spliced intron) + 16 behavior assertions across (in-memory, streaming) x 4 flag combos. Existing streaming-equivalence suite extended with test_streaming_matches_in_memory_with_flags parametrized over the same flag combos. tests/unit/test_filters.py updated to reflect corrected include_duplicates semantics in should_extract_sequences_for.
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Backport of the isoform-flag-parity fix from the v2.4.x maintenance line (v2.4.3) onto origin/main (v2.7.0).
The in-memory post-extraction filter hardcoded
longest_only=Trueandinclude_duplicates=False, ignoring CLI flags. The streaming per-contig worker hardcodedlongest_only=Trueand did not haveallow_multiple_isoformsplumbed into itsconfig_dict. The extraction prefiltershould_extract_sequences_foralways skipped coord-duplicates regardless ofinclude_duplicates. All three sites now consult config consistently; streaming/in-memory equivalence holds across all (-i,-d) flag combinations.Tests added: synthetic alt-isoform fixture (1 gene, 2 isoforms, 1 shared intron, 1 alt-spliced intron) + 16 behavior assertions across (in-memory, streaming) x 4 flag combos. Existing streaming-equivalence suite extended with
test_streaming_matches_in_memory_with_flagsparametrized over the same flag combos.tests/unit/test_filters.pyupdated to reflect correctedinclude_duplicatessemantics inshould_extract_sequences_for.