oxbow
Oxbow makes genomic data ready for high-performance analytics.
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Download Latest Version (.zip)- ci.yml
- pull_request_template.md
- release-python.yml
- release-rust.yml
- CODE_OF_CONDUCT.md
- dependabot.yaml
- favicon.ico
- icon_book.svg
- icon_branch.svg
- icon_code.svg
- logo.svg
- oxbow-arrow-diagram.svg
- oxbow-logo-wide-black.svg
- oxbow-logo-wide-white.svg
- oxbow-logo.svg
- style.css
- switcher.json
- version.html
- oxbow.arrow.BatchReaderDataset.rst
- oxbow.arrow.BatchReaderFragment.rst
- oxbow.core.BamFile.rst
- oxbow.core.BcfFile.rst
- oxbow.core.BedFile.rst
- oxbow.core.BigBedFile.rst
- oxbow.core.BigWigFile.rst
- oxbow.core.CramFile.rst
- oxbow.core.FastaFile.rst
- oxbow.core.FastqFile.rst
- oxbow.core.GffFile.rst
- oxbow.core.GtfFile.rst
- oxbow.core.PyBamScanner.rst
- oxbow.core.PyBBIZoomScanner.rst
- oxbow.core.PyBcfScanner.rst
- oxbow.core.PyBedScanner.rst
- oxbow.core.PyBigBedScanner.rst
- oxbow.core.PyBigWigScanner.rst
- oxbow.core.PyCramScanner.rst
- oxbow.core.PyFastaScanner.rst
- oxbow.core.PyFastqScanner.rst
- oxbow.core.PyGffScanner.rst
- oxbow.core.PyGtfScanner.rst
- oxbow.core.PySamScanner.rst
- oxbow.core.PyVcfScanner.rst
- oxbow.core.SamFile.rst
- oxbow.core.VcfFile.rst
- oxbow.from_bam.rst
- oxbow.from_bcf.rst
- oxbow.from_bed.rst
- oxbow.from_bigbed.rst
- oxbow.from_bigwig.rst
- oxbow.from_cram.rst
- oxbow.from_fasta.rst
- oxbow.from_fastq.rst
- oxbow.from_gff.rst
- oxbow.from_gtf.rst
- oxbow.from_sam.rst
- oxbow.from_vcf.rst
- oxbow.read_bam.rst
- oxbow.read_bcf.rst
- oxbow.read_bed.rst
- oxbow.read_bigbed.rst
- oxbow.read_bigwig.rst
- oxbow.read_cram.rst
- oxbow.read_fasta.rst
- oxbow.read_fastq.rst
- oxbow.read_gff.rst
- oxbow.read_gtf.rst
- oxbow.read_sam.rst
- oxbow.read_vcf.rst
- index.md
- python.rst
- r.md
- development.md
- documentation.md
- index.md
- data
- index.md
- installation.md
- quickstart.md
- why.md
- data
- index.md
- sam_mark_duplicates.md
- coordinate-systems.md
- index.md
- matrix.md
- conf.py
- index.rst
- autosql-sample.bb
- ENCFF758CQW.100.bed.gz
- example.gff
- example.gtf
- list.txt
- malformed.bam
- malformed.bb
- malformed.bcf
- malformed.bed
- malformed.bw
- malformed.cram
- malformed.fasta
- malformed.fastq
- malformed.gff
- malformed.gtf
- malformed.sam
- README.md
- sample-ref.cram
- sample-ref.cram.crai
- sample-ref.fa
- sample-ref.fa.fai
- sample-ref.sam
- sample.bam
- sample.bam.bai
- sample.bb
- sample.bcf
- sample.bcf.csi
- sample.bed
- sample.bed.gz
- sample.bed.gz.tbi
- sample.bw
- sample.cram
- sample.cram.crai
- sample.fasta
- sample.fasta.fai
- sample.fasta.gz
- sample.fasta.gz.gzi
- sample.fastq
- sample.fastq.bgz
- sample.fastq.bgz.gzi
- sample.fastq.gz
- sample.gff
- sample.gtf
- sample.sam
- sample.sam.gz
- sample.sam.gz.tbi
- sample.sorted.gff
- sample.sorted.gff.gz
- sample.sorted.gff.gz.tbi
- sample.sorted.gtf
- sample.sorted.gtf.gz
- sample.sorted.gtf.gz.tbi
- sample.ubam
- sample.ubcf
- sample.vcf
- sample.vcf.gz
- sample.vcf.gz.csi
- sample.vcf.gz.tbi
- batch.rs
- field.rs
- tag.rs
- query.rs
- stream.rs
- bam.rs
- batch_iterator.rs
- cram.rs
- sam.rs
- model.rs
- scanner.rs
- batch.rs
- field.rs
- batch.rs
- field.rs
- base.rs
- zoom.rs
- query.rs
- stream.rs
- query.rs
- stream.rs
- base.rs
- zoom.rs
- batch_iterator.rs
- bbizoom.rs
- bigbed.rs
- bigwig.rs
- model.rs
- scanner.rs
- batch.rs
- field.rs
- field_def.rs
- schema.rs
- query.rs
- stream.rs
- batch_iterator.rs
- bed.rs
- model.rs
- scanner.rs
- attribute.rs
- batch.rs
- field.rs
- query.rs
- stream.rs
- batch_iterator.rs
- gff.rs
- gtf.rs
- model.rs
- scanner.rs
- batch.rs
- field.rs
- query.rs
- stream.rs
- batch_iterator.rs
- fasta.rs
- fastq.rs
- model.rs
- scanner.rs
- index.rs
- query.rs
- batch.rs
- field.rs
- genotype.rs
- info.rs
- query.rs
- stream.rs
- batch_iterator.rs
- bcf.rs
- vcf.rs
- model.rs
- scanner.rs
- alignment.rs
- batch.rs
- bbi.rs
- bed.rs
- coords.rs
- error.rs
- gxf.rs
- lib.rs
- sequence.rs
- util.rs
- variant.rs
- Cargo.lock
- Cargo.toml
- LICENSE-APACHE
- LICENSE-MIT
- README.md
- bench.ipynb
- alignment.py
- base.py
- bbi.py
- bed.py
- gxf.py
- sequence.py
- variant.py
- __init__.py
- _filetypes.py
- _pyarrow.py
- arrow.py
- core.py
- py.typed
- alignment.rs
- bbi.rs
- bed.rs
- error.rs
- filelike.rs
- gxf.rs
- lib.rs
- sequence.rs
- util.rs
- variant.rs
- test_alignment.TestBamFile.test_batches.yaml
- test_alignment.TestBamFile.test_init_callstack.yaml
- test_alignment.TestCramFile.test_batches.yaml
- test_alignment.TestCramFile.test_init_callstack.yaml
- test_alignment.TestSamFile.test_batches.yaml
- test_alignment.TestSamFile.test_init_callstack.yaml
- test_bbi.TestBigBedFile.test_batches.yaml
- test_bbi.TestBigBedFile.test_init_callstack.yaml
- test_bbi.TestBigWigFile.test_batches.yaml
- test_bbi.TestBigWigFile.test_init_callstack.yaml
- test_bed.TestBedFile.test_batches.yaml
- test_bed.TestBedFile.test_init_callstack.yaml
- test_gxf.TestGffFile.test_batches.yaml
- test_gxf.TestGffFile.test_init_callstack.yaml
- test_gxf.TestGtfFile.test_batches.yaml
- test_gxf.TestGtfFile.test_init_callstack.yaml
- test_scanners.TestPyBamScanner.test_scan.yaml
- test_scanners.TestPyBamScanner.test_scan_invalid_field.yaml
- test_scanners.TestPyBcfScanner.test_chrom_names.yaml
- test_scanners.TestPyBcfScanner.test_chrom_sizes.yaml
- test_scanners.TestPyBcfScanner.test_genotype_field_defs.yaml
- test_scanners.TestPyBcfScanner.test_info_field_defs.yaml
- test_scanners.TestPyBcfScanner.test_scan.yaml
- test_scanners.TestPyBcfScanner.test_scan_invalid_field.yaml
- test_scanners.TestPyBcfScanner.test_scan_query.yaml
- test_scanners.TestPyBedScanner.test_scan.yaml
- test_scanners.TestPyBedScanner.test_scan_invalid_field.yaml
- test_scanners.TestPyBigBedScanner.test_scan.yaml
- test_scanners.TestPyBigBedScanner.test_scan_invalid_field.yaml
- test_scanners.TestPyBigBedScanner.test_scan_with_autosql.yaml
- test_scanners.TestPyBigWigScanner.test_scan.yaml
- test_scanners.TestPyBigWigScanner.test_scan_invalid_field.yaml
- test_scanners.TestPyFastaScanner.test_scan.yaml
- test_scanners.TestPyFastaScanner.test_scan_invalid_field.yaml
- test_scanners.TestPyFastaScanner.test_scan_query.yaml
- test_scanners.TestPyFastqScanner.test_scan.yaml
- test_scanners.TestPyFastqScanner.test_scan_invalid_field.yaml
- test_scanners.TestPyGffScanner.test_scan.yaml
- test_scanners.TestPyGffScanner.test_scan_query_sorted_compressed.yaml
- test_scanners.TestPyGffScanner.test_scan_sorted.yaml
- test_scanners.TestPyGffScanner.test_scan_sorted_compressed.yaml
- test_scanners.TestPyGffScanner.test_scan_with_attributes.yaml
- test_scanners.TestPyGtfScanner.test_scan.yaml
- test_scanners.TestPyGtfScanner.test_scan_query_sorted_compressed.yaml
- test_scanners.TestPyGtfScanner.test_scan_sorted.yaml
- test_scanners.TestPyGtfScanner.test_scan_sorted_compressed.yaml
- test_scanners.TestPyGtfScanner.test_schema.yaml
- test_scanners.TestPyGtfScanner.test_schema_with_fields.yaml
- test_scanners.TestPySamScanner.test_scan.yaml
- test_scanners.TestPySamScanner.test_scan_invalid_field.yaml
- test_scanners.TestPyVcfScanner.test_chrom_names.yaml
- test_scanners.TestPyVcfScanner.test_chrom_names_compressed.yaml
- test_scanners.TestPyVcfScanner.test_chrom_sizes.yaml
- test_scanners.TestPyVcfScanner.test_chrom_sizes_compressed.yaml
- test_scanners.TestPyVcfScanner.test_genotype_field_defs.yaml
- test_scanners.TestPyVcfScanner.test_genotype_field_defs_compressed.yaml
- test_scanners.TestPyVcfScanner.test_genotype_field_names.yaml
- test_scanners.TestPyVcfScanner.test_genotype_field_names_compressed.yaml
- test_scanners.TestPyVcfScanner.test_info_field_defs.yaml
- test_scanners.TestPyVcfScanner.test_info_field_defs_compressed.yaml
- test_scanners.TestPyVcfScanner.test_info_field_names.yaml
- test_scanners.TestPyVcfScanner.test_info_field_names_compressed.yaml
- test_scanners.TestPyVcfScanner.test_scan.yaml
- test_scanners.TestPyVcfScanner.test_scan_compressed.yaml
- test_scanners.TestPyVcfScanner.test_scan_invalid_field.yaml
- test_scanners.TestPyVcfScanner.test_scan_query.yaml
- test_sequence.TestFastaFile.test_batches.yaml
- test_sequence.TestFastaFile.test_batches_with_regions.yaml
- test_sequence.TestFastaFile.test_init_callstack.yaml
- test_sequence.TestFastqFile.test_batches.yaml
- test_sequence.TestFastqFile.test_init_callstack.yaml
- test_variant.TestBcfFile.test_batches.yaml
- test_variant.TestBcfFile.test_init_callstack.yaml
- test_variant.TestVcfFile.test_batches.yaml
- test_variant.TestVcfFile.test_init_callstack.yaml
- conftest.py
- data
- test_alignment.py
- test_base.py
- test_bbi.py
- test_bed.py
- test_coords.py
- test_gxf.py
- test_pyarrow.py
- test_scanners.py
- test_sequence.py
- test_variant.py
- utils.py
- wiretap.py
- Cargo.toml
- pyproject.toml
- README.md
- uv.lock
- api.R
- extendr-wrappers.R
- lib.rs
- Cargo.toml
- oxbow
- .gitignore
- entrypoint.c
- Makevars
- Makevars.ucrt
- Makevars.win
- oxbow-win.def
- DESCRIPTION
- NAMESPACE
- README.md
- .gitattributes
- .gitignore
- .readthedocs.yaml
- Cargo.lock
- Cargo.toml
- LICENSE-APACHE
- LICENSE-MIT
- README.md
- rust-toolchain.toml
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