Feat/expression anchors#13
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The assemble_sequences_with_anchors function is implemented and working.
Summary of Changes
Rust (src/expressions.rs:325-410):
- Added assemble_sequences_with_anchors_expr function
- Takes 3 input series: sequences, start_anchor, end_anchor
- Extracts anchor strings from first row of each anchor column
- Only supports shortest_path method (compression/auto don't need
anchors)
Python (rogtk/__init__.py:155-231):
- Added assemble_sequences_with_anchors() wrapper function
- Takes expr, start_anchor_col, end_anchor_col as expression arguments
- Same kwargs as original: k, min_coverage, method, etc.
Usage
segments.group_by(['umi', 'start_meta', 'end_meta']).agg(
rogtk.assemble_sequences_with_anchors(
expr=pl.col('segment_seq'),
start_anchor_col=pl.first('start_meta_seq'),
end_anchor_col=pl.first('end_meta_seq'),
k=15,
min_coverage=20,
).alias('consensus_seq')
)
Add Rust expressions and Python wrappers to extract actual insertion sequences from CIGAR strings and enrich cassiopeia allele notation. Rust (src/expressions.rs): - extract_insertions_from_cigar(): Parse CIGAR to extract insertion sequences - enrich_allele_with_insertions(): Transform [pos:NI] to [pos:NI:SEQ] - enrich_allele_insertions_expr: Polars expression (allele, seq, cigar) - extract_cigar_insertions_expr: Polars expression (seq, cigar) - Handle 1-based to 0-based position conversion for allele notation Python (rogtk/__init__.py): - CigarNamespace: Registered as pl.Expr.cigar namespace - enrich_insertions(): Method to enrich allele strings - extract_cigar_insertions(): Standalone function for extraction Example: [78:5I] → [78:5I:ACTTA]
Process multiple BAM files into a single parquet file with bounded
memory.
Streams batches sequentially from each BAM, writing directly to parquet
without intermediate files or memory spikes.
Features:
- Bounded memory usage via batch streaming (configurable batch_size)
- Optional source_file column to track origin BAM per record
- Input validation, progress reporting, and Python interrupt handling
- Supports all existing options (compression, sequence/quality
inclusion, limit)
Performance: ~43k records/sec (1.86M records from 46 BAMs in 43s)
Usage:
rogtk.bams_to_parquet(bam_list, "output.parquet",
include_source_file=True)
lf = pl.scan_parquet("output.parquet") # lazy interface for
downstream ops
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