polars-bio
Blazing-Fast Bioinformatic Operations on Python DataFrames
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최종 버전 다운로드 (.zip)- config.toml
- apply.md
- archive.md
- proposal.md
- bench_pushdown.py
- SKILL.md
- linkedin-template.md
- SKILL.md
- devcontainer.json
- Dockerfile
- bug_report.yml
- config.yml
- documentation.yml
- feature_request.yml
- benchmark.yml
- claude-code-review.yml
- claude.yml
- publish_documentation.yml
- publish_to_pypi.yml
- release.yml
- PULL_REQUEST_TEMPLATE.md
- ARCHITECTURE.md
- CONCERNS.md
- CONVENTIONS.md
- INTEGRATIONS.md
- STACK.md
- STRUCTURE.md
- TESTING.md
- 01-01-PLAN.md
- 01-01-SUMMARY.md
- 01-02-PLAN.md
- 01-CONTEXT.md
- 01-RESEARCH.md
- ARCHITECTURE.md
- FEATURES.md
- PITFALLS.md
- STACK.md
- SUMMARY.md
- config.json
- PROJECT.md
- REQUIREMENTS.md
- ROADMAP.md
- STATE.md
- bench_wallcpu.sh
- both2.sh
- correctness_verify.sh
- gen_post.py
- matched_bench2.sh
- mem_measure.sh
- parse_all.py
- parse_drift.py
- pb_mem.py
- pb_one.py
- pb_reps.py
- pb_wallcpu.py
- pbk.sh
- pbt2.py
- rebin_compare.py
- reps.sh
- rq_scaling.sh
- run_all.sh
- run_drift.sh
- thread_invariance.sh
- bench.py
- parity.py
- compare_benchmark_results.sh
- generate_comparison_charts.py
- generate_interactive_comparison.py
- parse_benchmark_results.py
- README_BENCHMARKS.md
- recipe.yaml
- build.sh
- meta.yaml
- README.md
- auxiliary.md
- index.md
- operations.md
- reading.md
- sql.md
- writing.md
- polars-bio-overlap-mem.png
- polars-bio-overlap-pd-mem.png
- polars-bio-overlap-pl-mem.png
- bioframe.png
- bioframe_sink.png
- polars-bio.png
- polars-bio_sink.png
- polars-bio_stream_sink.png
- pyranges0.png
- pyranges0_sink.png
- pyranges1.png
- pyranges1_sink.png
- count-overlaps-parallel.png
- count-overlaps-single.png
- coverage-parallel.png
- coverage-single.png
- eccb-2026.png
- format-bam.png
- format-fastq.png
- format-scaling.png
- format-vcf.png
- logo-large-dark.png
- logo-large.png
- logo.png
- nearest-parallel.png
- nearest-single.png
- overlap-parallel.png
- overlap-single.png
- results-nearest-0.1.1.png
- results-overlap-0.1.1.png
- summary-results.png
- bcf-reader-memory.png
- bcf-reader-time.png
- bcf-thread-scaling.png
- all_operations_speedup_comparison.png
- polars_bio_scalability_8_7.png
- all_operations_walltime_comparison.png
- bench-20250-all_operations_speedup_comparison.png
- bench_parallel_speedup_combined_8-7.png
- benchmark_comparison_genomicranges_vs_polars_bio.png
- benchmark_speedup_comparison_genomicranges_vs_polars_bio.png
- combined_benchmark_visualization.png
- combined_multi_testcase.png
- star-history-202595.png
- one_thread_all_operations_2_1.png
- one_thread_all_operations_8_7.png
- thread_scalability_cluster.png
- thread_scalability_complement.png
- thread_scalability_count_overlaps.png
- thread_scalability_coverage.png
- thread_scalability_merge.png
- thread_scalability_nearest.png
- thread_scalability_overlap.png
- thread_scalability_subtract.png
- bam_with_tags.png
- bam_without_tags.png
- fastq_comparison.png
- thread_scaling.png
- vcf_with_info.png
- vcf_without_info.png
- bcf-one-thread.png
- bgen-one-thread.png
- bgen-scaling.png
- pgen-one-thread.png
- scaling-all-formats.png
- general_performance.png
- memory_comparison.png
- seminar.png
- thread_scalability.png
- version_comparison.png
- bcf-genotype-readers-2026-08.md
- benchmark-operations-2025-09.md
- benchmark-operations-2026-02.md
- dataframe-paths-benchmark-2026-04.md
- fastqc-benchmark-2026-07.md
- genomic-formats-benchmark-2026-02.md
- genomic-formats-benchmark-2026-07.md
- gff-read-optimizations-2025-09.md
- release-0.23.0.md
- release-0.26.0.md
- release-0.31.0-vcf-zarr.md
- rewriting-bioinformatics-2026-07.md
- index.md
- cloud.md
- dataframes.md
- index.md
- operations.md
- parallel.md
- reading.md
- sql.md
- writing.md
- .part-00000-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet.crc
- .part-00001-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet.crc
- _SUCCESS
- part-00000-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet
- part-00001-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet
- .part-00000-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet.crc
- .part-00001-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet.crc
- _SUCCESS
- part-00000-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet
- part-00001-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet
- example.bam
- example.bed.bgz
- example.fastq.gz
- example.gff3.bgz
- example.vcf
- tutorial.ipynb
- extra.css
- 2026-05-08-vcf-zarr-implementation.md
- 2026-05-09-vcf-zarr-benchmark-notebook-implementation.md
- 2026-05-10-vcf-zarr-typed-values-implementation.md
- 2026-06-26-gff-gtf-attributes-sentinel.md
- 2026-06-27-robust-predicate-pushdown.md
- 2026-07-02-fastqc-per-tile-and-kmer.md
- 2026-07-02-fastqc-phase1-vertical-slice.md
- 2026-08-17-pgen-polars-bio-binding.md
- 2026-05-08-vcf-zarr-design.md
- 2026-05-09-vcf-zarr-benchmark-notebook-design.md
- 2026-06-26-gff-gtf-attributes-sentinel-design.md
- 2026-06-27-robust-predicate-pushdown-design.md
- 2026-07-01-mimalloc-allocator-impact-design.md
- 2026-07-02-fastqc-datafusion-udtf-design.md
- 2026-07-02-fastqc-per-tile-and-kmer-design.md
- 2026-07-04-rewriting-bioinformatics-blog-design.md
- 2026-07-27-adoption-zero-config-first-run-design.md
- 2026-08-17-pgen-polars-bio-binding-design.md
- contact.md
- developers.md
- faq.md
- index.md
- performance.md
- quickstart.md
- requirements.txt
- supplement.md
- talks.md
- versions.json
- .env
- start.sh
- stop.sh
- policy-anonymous.json
- policy-priv.json
- test.fasta
- vep.vcf
- vep.vcf.bgz
- docker-compose.yml
- it_ensembl_vcf_bgz.py
- it_object_storage_io.py
- README.md
- feature_counting_benchmark.ipynb
- vcf_zarr_benchmark.ipynb
- vcf_zarr_small_benchmark.ipynb
- spec.md
- design.md
- proposal.md
- tasks.md
- spec.md
- design.md
- proposal.md
- tasks.md
- spec.md
- proposal.md
- tasks.md
- spec.md
- design.md
- proposal.md
- tasks.md
- spec.md
- design.md
- proposal.md
- tasks.md
- spec.md
- design.md
- proposal.md
- tasks.md
- spec.md
- design.md
- proposal.md
- tasks.md
- spec.md
- design.md
- proposal.md
- tasks.md
- spec.md
- proposal.md
- tasks.md
- spec.md
- design.md
- proposal.md
- tasks.md
- spec.md
- design.md
- proposal.md
- tasks.md
- spec.md
- proposal.md
- tasks.md
- spec.md
- AGENTS.md
- project.md
- header.html
- __init__.py
- _metadata.py
- _path_utils.py
- constants.py
- context.py
- exceptions.py
- fastqc_op.py
- interval_op_helpers.py
- io.py
- logging.py
- metadata_extractors.py
- operations.py
- pileup_op.py
- polars_ext.py
- predicate_translator.py
- pushdown.py
- range_op.py
- range_op_helpers.py
- range_op_io.py
- range_utils.py
- sql.py
- sql_predicate_builder.py
- utils.py
- generate_benchmark_metadata.py
- generate_dataframe_paths_benchmark_figures.py
- update_benchmark_index.py
- context.rs
- fastqc.rs
- lib.rs
- operation.rs
- option.rs
- pileup.rs
- query.rs
- scan.rs
- utils.rs
- write.rs
- reads.csv
- targets.csv
- reads.csv
- targets.csv
- .part-00000-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet.crc
- .part-00001-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet.crc
- _SUCCESS
- part-00000-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet
- part-00001-47fafbb5-1cab-410c-9461-d10effacf760-c000.snappy.parquet
- .part-00000-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet.crc
- .part-00001-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet.crc
- _SUCCESS
- part-00000-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet
- part-00001-a0d75244-2d87-41eb-a3eb-a18847c7cb87-c000.snappy.parquet
- 10x_pbmc_tags.bam
- 10x_pbmc_tags.bam.bai
- mapq255.bam
- multi_chrom.bam
- multi_chrom.bam.bai
- NA12878_10k.bam
- NA12878_10k.bam.bai
- NA12878_10k_samtools_depth.tsv.gz
- nanopore_custom_tags.bam
- nanopore_custom_tags.bam.bai
- test.bam
- test.bam.bai
- annotations.bb
- annotations.bed
- chrom.sizes
- large_signal.bw
- signal.bedgraph
- signal.bw
- VALIDATION.md
- antku_small.bcf
- antku_small.bcf.csi
- ensembl-2.bcf
- ensembl-2.bcf.csi
- ensembl.bcf
- genotype_missing.bcf
- genotype_missing.bcf.csi
- info_bare_key.bcf
- info_bare_key.bcf.csi
- info_bare_key_realdata.bcf
- info_bare_key_realdata.bcf.csi
- info_invalid_flag_value.bcf
- info_invalid_flag_value.bcf.csi
- info_missing_array.bcf
- info_missing_array.bcf.csi
- multi_chrom.bcf
- multi_chrom.bcf.csi
- multisample.bcf
- multisample.bcf.csi
- multisample_large.bcf
- multisample_large.bcf.csi
- README.md
- single_sample_collision.bcf
- single_sample_collision.bcf.csi
- vep.bcf
- vep.bcf.csi
- vep_annotate_test.bcf
- vep_annotate_test.bcf.csi
- chr16_fragile_site.bed
- chr16_fragile_site.bed.bgz
- ENCFF001XKR.bed.gz
- test.bed
- missing_calls.bgen
- multisample.bgen
- multisample.sample
- chr20.fa
- chr20.fa.fai
- test_chr20.cram
- huffman_byte_encoding.cram
- multi_chrom.cram
- multi_chrom.cram.crai
- nanopore_custom_tags.cram
- nanopore_custom_tags.cram.crai
- test.cram
- test.cram.crai
- example.fasta
- test.fasta
- adapter_mix.nogroup.fastqc_data.txt
- dup_mix.nogroup.fastqc_data.txt
- example.nogroup.fastqc_data.txt
- kmer_mix.nogroup.kmers.fastqc_data.txt
- per_tile_mix.nogroup.fastqc_data.txt
- adapter_mix.fastq
- dup_mix.fastq
- example.fastq
- example.fastq.bgz
- example.fastq.bgz.gzi
- example.fastq.gz
- kmer_mix.fastq
- multimember_clean.fastq.gz
- multimember_pigz.fastq.gz
- multimember_split.fastq.gz
- per_tile_mix.fastq
- sample_no_index.fastq.bgz
- sample_parallel.fastq.bgz
- sample_parallel.fastq.bgz.gzi
- test.fastq
- wrong_extension.fastq.gz
- 1_multi_chrom.gff3.gz
- 1_multi_chrom.gff3.gz.tbi
- chrY_test_subset.gff3.bgz
- gencode.v38.annotation.gff3
- gencode.v38.annotation.gff3.bgz
- gencode.v38.annotation.gff3.bgz.gzi
- gencode.v38.annotation.gff3.gz
- multi_chrom.gff3.gz
- multi_chrom.gff3.gz.tbi
- wrong_extension.gff3.gz
- test.gtf
- multi_chrom.pairs.gz
- multi_chrom.pairs.gz.tbi
- test.pairs
- dosage.pgen
- dosage.psam
- dosage.pvar
- oracle.pgen
- oracle.psam
- oracle.pvar
- phase.pgen
- phase.psam
- phase.pvar
- unused_alt.pgen
- unused_alt.psam
- unused_alt.pvar
- test.sam
- antku_small.vcf.gz
- ensembl-2.vcf
- ensembl.vcf
- genotype_missing.vcf
- info_bare_key.vcf
- info_bare_key_realdata.vcf
- info_invalid_flag_value.vcf
- info_missing_array.vcf
- multi_chrom.vcf.gz
- multi_chrom.vcf.gz.tbi
- multisample.vcf
- multisample.vcf.gz
- single_sample_collision.vcf
- vep.vcf
- vep.vcf.bgz
- vep.vcf.gz
- vep_annotate_test.vcf
- wrong_extension.vcf.bgz
- wrong_extension.vcf.gz
- .zarray
- .zattrs
- 0
- .zarray
- .zattrs
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- .zarray
- .zattrs
- 0
- .zarray
- .zattrs
- 0
- .zattrs
- .zgroup
- input.csv
- reads.csv
- targets.csv
- reads.csv
- targets.csv
- _expected.py
- conftest.py
- test_bcf_io.py
- test_bgen_io.py
- test_bioframe.py
- test_comprehensive_metadata.py
- test_context_options.py
- test_coordinate_system_metadata.py
- test_custom_tag_inference.py
- test_execution_plan_validation.py
- test_fasta_write.py
- test_fastq_write.py
- test_fastqc.py
- test_fastqc_correctness.py
- test_fastqc_golden.py
- test_fastqc_parity.py
- test_filter_select_attributes_bug_fix.py
- test_gff_eager_vs_lazy.py
- test_io.py
- test_io_bam.py
- test_io_bbi.py
- test_io_bbi_parity.py
- test_io_bbi_parity_dependency.py
- test_io_bbi_streaming.py
- test_io_bed.py
- test_io_cram.py
- test_io_cram_huffman.py
- test_io_fasta.py
- test_io_fastq.py
- test_io_gff.py
- test_io_gtf.py
- test_io_indexed.py
- test_io_pairs.py
- test_io_vcf.py
- test_issue_395_eager_lazy_segfault.py
- test_lazy_streaming_fix.py
- test_lazyframe_partitioning.py
- test_native.py
- test_optimization_bug_fix.py
- test_overlap_algorithms.py
- test_overlap_output_mode.py
- test_pandas.py
- test_parallel_io.py
- test_partitioned_range_operation_regressions.py
- test_pgen_io.py
- test_pileup.py
- test_pileup_samtools.py
- test_polars.py
- test_polars_bio_projection_validation.py
- test_polars_ext.py
- test_predicate_in_between.py
- test_predicate_pushdown.py
- test_predicate_pushdown_chrY_start.py
- test_predicate_translator_units.py
- test_projection_performance.py
- test_projection_pushdown.py
- test_pushdown_equivalence.py
- test_pushdown_helpers.py
- test_source_metadata.py
- test_streaming.py
- test_suffix_handling.py
- test_user_scenario.py
- test_vcf_format_columns.py
- test_vcf_info_bare_keys.py
- test_vcf_info_missing_values.py
- test_vcf_parsing.py
- test_vcf_projection_pushdown.py
- test_vcf_read_options.py
- test_vcf_write.py
- test_vcf_zarr_io.py
- test_warnings.py
- test_wide_dataframes.py
- .gitignore
- .pre-commit-config.yaml
- .readthedocs.yaml
- AGENTS.md
- Cargo.lock
- Cargo.toml
- CHANGELOG.md
- CLAUDE.md
- CODE_OF_CONDUCT.md
- HANDOVER-pgen-benchmarks.md
- HANDOVER-pgen-perf.md
- LICENSE
- Makefile
- mkdocs.yml
- polars-bio.iml
- pyproject.toml
- README.md
- requirements.txt
- rust-toolchain.toml
- rustfmt.toml
- uv.lock
// repository documentation
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