oxbow
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abdenlab
Read specialized NGS formats as data frames in R, Python, and more.
It would be great if read_bam worked without a BAM index (provided you're not doing a region query). My use case: Oxford Nanopore's Dorado basecaller outputs basecalled reads in BAM...
Oxbow's Python functions (read_bam, etc.) currently return a bytes object. It would be great if they instead returned an iterator of pa.RecordBatch objects instead. The goal here would be to...
This PR handles spec compliant BED12 files, so it won't work as is with BED3-9 and optional fields. Handling the other types of bed files could require creating separate reader...
Partially implemented (some may already be implemented) - [ ] alignments: - [ ] sam.gz: - [ ] tbi - [ ] csi - [ ] bam: bai/csi - [x]...
The fasta implementation was a little tricky since there are multiple relevant readers upstream in noodles: `fasta::Reader`, `fasta::IndexedReader`, and `fasta::fai::Reader`. The core `records_to_ipc` function relies on the `query` method supplied...
Added an API function that returns the reference sequences from the bam file. Example usage: ``` f = open('my.bam', 'r') ipc = ox.read_bam_references(f) pl.read_ipc(ipc) ``` This returns a polars dataframe...
