feat: add class to generate pileup over AlignedSegments #1353
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nh13
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Jul 4, 2025
| cdef class IteratorColumnAll(IteratorColumn): | ||
| pass | ||
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| cdef class IteratorColumnRecords: |
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this cannot extend IteratorColumn since IteratorColumn requires a SAM file.
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I've now finally finished up and merged #1362. Can I interest you in rebasing this onto current master and ideally updating it to use |
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…ents Add new IteratorColumnRecords class that generates pileup columns from a collection of AlignedSegment objects using htslib's push-based pileup API (bam_plp_push/bam_plp64_next). Key features: - Accepts any iterable of AlignedSegments (requires coordinate-sorted order) - Supports optional reference sequence (fastafile parameter) - Includes add_reference(), has_reference(), and seq_len property - Configurable min_base_quality parameter - Uses 64-bit position types (hts_pos_t) for extended chromosome support Implementation notes: - Uses bam_plp_push/bam_plp64_next instead of callback-based approach - Records consumed during initialization for push-based API - Includes required NULL push to signal end-of-input - Leverages 64-bit APIs (bam_plp64_next, faidx_fetch_seq64) from PR pysam-developers#1362 - Uses opaque bam_plp_s struct (no direct field access needed) Testing: - 12 new tests covering reference support, edge cases, and parameters - Documented known limitation: minor depth differences vs samtools mpileup due to push-based vs pull-based filtering differences Changes: - Add IteratorColumnRecords class in pysam/libcalignmentfile.pyx - Update to use 64-bit pileup APIs (bam_plp64_next, faidx_fetch_seq64) - Add type stub in pysam/libcalignmentfile.pyi - Add parameterized to test dependencies for parameterized tests - Update CI workflows to install parameterized package Closes pysam-developers#1352
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@jmarshall done! Ready for re-review! |
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@jmarshall bump! |
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I know 😄 — It's on the short list! |
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Add new IteratorColumnRecords class that generates pileup columns from a
collection of AlignedSegment objects using htslib's push-based pileup API
(bam_plp_push/bam_plp64_next).
Key features:
Implementation notes:
Testing:
due to push-based vs pull-based filtering differences
Changes:
Closes #1352