Files in Rduckhts
'DuckDB' High Throughput Sequencing File Formats Reader Extension
configure
MD5
NEWS.md
NAMESPACE
DESCRIPTION
cleanup.win
configure.win
cleanup
R/geno.R
R/extension_metadata.R
R/htslib.R
R/catalog.R
R/duckhts.R
R/connection.R
R/count_mixture_lowpass.R
R/package_paths.R
R/ancestry_panel.R
R/sql_helpers.R
R/depth.R
R/ancestry_geno.R
R/ancestry_bam.R
R/convert_parquet.R
R/roh.R
R/ancestry_wide.R
R/ancestry.R
R/source_manifest.R
R/insert_size.R
R/package.R
R/bootstrap.R
R/build.R
R/somalier.R
R/load_compat.R
R/simd.R
R/somalier_find_sites.R
R/type_helpers.R
src/init.c
inst/htslib_config.R.in
inst/COPYRIGHT
inst/WORDLIST
inst/extdata/ce.fa.fai
inst/extdata/empty-tids.bed
inst/extdata/bam_mismatch.cram
inst/extdata/rg.sam.gz.tbi
inst/extdata/geno_ps_type.vcf.gz
inst/extdata/score_chrprefix.vcf
inst/extdata/bcf_offset.bcf.csi
inst/extdata/vcf_file.bcf.csi
inst/extdata/geno_sites.vcf.gz.tbi
inst/extdata/bam_scan_mixed.cram
inst/extdata/liftover_clip_pad.chain
inst/extdata/geno_calls.bcf
inst/extdata/meta_tabix.tsv.gz.tbi
inst/extdata/bcf_scan_contigs.empty.bcf.csi
inst/extdata/rg.sam.gz
inst/extdata/range.cram.crai
inst/extdata/bam_scan_mixed.bam
inst/extdata/parallel_empty_contigs.vcf.gz.tbi
inst/extdata/geno_format_case.vcf
inst/extdata/bam_scan_mixed.bam.csi
inst/extdata/bam_scan_all_unplaced.cram.crai
inst/extdata/bcf_scan_contigs.bcf
inst/extdata/interleaved.fq
inst/extdata/somalier_sites.vcf
inst/extdata/fixed_count_arrays.vcf
inst/extdata/track.bed
inst/extdata/parallel_empty_contigs.bam.bai
inst/extdata/bam_scan_empty.cram
inst/extdata/parallel_empty_contigs.vcf.gz
inst/extdata/targets.bed
inst/extdata/liftover_clip_pad_src.fa.fai
inst/extdata/bcf_offset_plain.vcf
inst/extdata/score_summary_smallp.tsv
inst/extdata/ovl.bam.bai
inst/extdata/gff_file.gff.gz.tbi
inst/extdata/geno_format.vcf.gz.tbi
inst/extdata/gff_file.gff.gz
inst/extdata/geno_sites.vcf.gz
inst/extdata/region_union.bcf
inst/extdata/unordered.bed
inst/extdata/bam_scan_empty.bam.csi
inst/extdata/bcf_scan_contigs.partial.vcf.gz.index.tbi
inst/extdata/geno_calls.vcf.gz
inst/extdata/bcf_cache_lifecycle.vcf
inst/extdata/score_targets.txt
inst/extdata/liftover_star_swap_src.fa.fai
inst/extdata/bam_scan_empty.cram.crai
inst/extdata/fixture_single.bam.bai
inst/extdata/liftover_repeat_dst.fa.fai
inst/extdata/gff_named_attributes.gff3.gz.tbi
inst/extdata/geno_ps_type.vcf
inst/extdata/header_tabix.tsv.gz
inst/extdata/bam_scan_mixed.bam.bai
inst/extdata/score_gwas_summary.vcf
inst/extdata/score_summary_pgs.tsv
inst/extdata/bam_scan_all_unplaced.bam.legacy.bai
inst/extdata/geno_sites.vcf
inst/extdata/bcf_scan_contigs.shifted.bcf
inst/extdata/mapping_number_families.vcf
inst/extdata/bam_mismatch.fa.fai
inst/extdata/gff_strict_invalid_attr.gff3
inst/extdata/score_summary_CNT.tsv
inst/extdata/bcf_offset.vcf.gz
inst/extdata/bcf_scan_contigs.empty.bcf
inst/extdata/gff_strict_invalid.gff3
inst/extdata/nuc_with_n.fa
inst/extdata/bam_scan_all_unplaced.cram
inst/extdata/bcf_scan_contigs.vcf
inst/extdata/bcf_scan_contigs.empty.vcf.gz.index.csi
inst/extdata/liftover_clip_pad_dst.fa.fai
inst/extdata/region_union.vcf
inst/extdata/bam_scan_mixed.bam.legacy.bai
inst/extdata/bam_read_groups.sam
inst/extdata/liftover_repeat_src.fa.fai
inst/extdata/bcf_scalar_counts.bcf.csi
inst/extdata/parallel_empty_contigs.bcf
inst/extdata/bam_scan_single.cram
inst/extdata/aux_tags.sam.gz
inst/extdata/bcf_info_type_clash.bcf
inst/extdata/score_summary_bolt.tsv
inst/extdata/geno_ps_width.vcf
inst/extdata/fastq_multiline.fq
inst/extdata/geno_ps_number.vcf.gz
inst/extdata/bcf_scan_contigs.shifted.vcf.gz.index.csi
inst/extdata/geno_format_case.bcf
inst/extdata/liftover_star_refadd_src.fa
inst/extdata/liftover_chr23_alias.chain
inst/extdata/gtf_named_attributes.gtf
inst/extdata/region_names.fa.fai
inst/extdata/bcf_scan_contigs.shifted.bcf.csi
inst/extdata/geno_sites.bcf.csi
inst/extdata/geno_ps_width.bcf
inst/extdata/gff_strict_invalid_end.gff3
inst/extdata/score_missing_ds.vcf
inst/extdata/score_missing_gt.vcf
inst/extdata/tidy_chunk_boundary.vcf
inst/extdata/test_vep_types.vcf
inst/extdata/bam_scan_all_unplaced.bam.bai
inst/extdata/bcf_scan_contigs.empty.vcf.gz
inst/extdata/roh_af.tsv.gz
inst/extdata/geno_format.bcf.csi
inst/extdata/score_regions.txt
inst/extdata/parallel_empty_contigs.bam
inst/extdata/score_summary_regenie.tsv
inst/extdata/bcf_scan_contigs.full.vcf.gz
inst/extdata/roh_single_site.vcf
inst/extdata/genbank_phase.gb
inst/extdata/liftover_chr23_alias_dst.fa
inst/extdata/geno_calls.vcf
inst/extdata/region_names.fa.gz.gzi
inst/extdata/somalier_brace.bam
inst/extdata/vcfpp_manifest.tsv
inst/extdata/phix174.gb
inst/extdata/nanopore.bam
inst/extdata/somalier_population_1000g.vcf.gz
inst/extdata/liftover_repeat_dst.fa
inst/extdata/fastq_long_qname.fq
inst/extdata/parallel_empty_contigs.bcf.csi
inst/extdata/bam_scan_single.bam.legacy.csi
inst/extdata/libbigwig_test.bw
inst/extdata/gtf_named_attributes.gtf.gz.tbi
inst/extdata/full-fragment-pairs.bam.bai
inst/extdata/range.cram
inst/extdata/somalier_brace.fa.fai
inst/extdata/bcf_scan_contigs.partial.vcf.gz.index.csi
inst/extdata/bcf_info_str_clash.bcf
inst/extdata/liftover_nw_limit_dst.fa
inst/extdata/r2.fq
inst/extdata/geno_sites.bcf
inst/extdata/score_columns.tsv
inst/extdata/bcf_scan_contigs.shifted.vcf.gz.index.tbi
inst/extdata/score_summary_metal.tsv
inst/extdata/colheaders.tsv
inst/extdata/bam_scan_single.bam.bai
inst/extdata/geno_ps_number.vcf
inst/extdata/range.bam.bai
inst/extdata/fixture_ref.fa.fai
inst/extdata/bam_scan_empty.bam
inst/extdata/nuc_with_n.bed
inst/extdata/header_tabix.tsv.gz.tbi
inst/extdata/somalier_brace.fa
inst/extdata/bcf_filter_list_regression.vcf
inst/extdata/bcf_scan_contigs.none.vcf.gz.index.tbi
inst/extdata/bam_offset_uncompressed.bam
inst/extdata/score_input.vcf
inst/extdata/bcf_scalar_counts.vcf
inst/extdata/bam_record_ends.tsv
inst/extdata/empty-tids.bam
inst/extdata/bam_scan_mixed.bam.nostats.legacy.bai
inst/extdata/liftover_star_swap_dst.fa.fai
inst/extdata/fixture_single.bam
inst/extdata/test_vep.vcf
inst/extdata/region_union.vcf.gz
inst/extdata/overlapping-pairs.bam.bai
inst/extdata/geno_format.bcf
inst/extdata/geno_calls.vcf.gz.tbi
inst/extdata/gff_named_attributes.gff3
inst/extdata/geno_raw_gt.vcf
inst/extdata/spec_standard_corrections.vcf
inst/extdata/meta_tabix.tsv.gz
inst/extdata/bam_scan_empty.bam.legacy.csi
inst/extdata/liftover_star_refadd_src.fa.fai
inst/extdata/roh_map_chr1.txt
inst/extdata/liftover_clip_pad_dst.fa
inst/extdata/bcf_offset.bcf
inst/extdata/bam_scan_single.cram.crai
inst/extdata/fixture_mixed_regions.bed
inst/extdata/bcf_scan_contigs.none.vcf.gz.index.csi
inst/extdata/gff_strict_extra_field.gff3
inst/extdata/roh_fixture.vcf.gz
inst/extdata/fixture_paired.bam
inst/extdata/fixture_mixed.cram
inst/extdata/score_summary_plink2.tsv
inst/extdata/bcf_scan_contigs.full.vcf.gz.index.tbi
inst/extdata/roh_repeated.vcf.gz.tbi
inst/extdata/liftover_repeat.chain
inst/extdata/bam_scan_mixed.bam.nostats.bai
inst/extdata/bcf_literal_contigs.vcf.gz.tbi
inst/extdata/somalier_brace.bam.bai
inst/extdata/score_summary_ssf.tsv
inst/extdata/bam_scan_single.bam
inst/extdata/liftover_chr23_alias_dst.fa.fai
inst/extdata/bam_mismatch.bam.bai
inst/extdata/bad.bed
inst/extdata/geno_phase_partial.vcf
inst/extdata/score_as.vcf
inst/extdata/bcf_scalar_counts.vcf.gz.tbi
inst/extdata/bam_scan_empty.bam.bai
inst/extdata/legacy_phred64.fq
inst/extdata/liftover_star_swap_src.fa
inst/extdata/empty-tids.bam.bai
inst/extdata/geno_format_case.vcf.gz
inst/extdata/big.bam
inst/extdata/score_summary.tsv
inst/extdata/bam_offset.sam
inst/extdata/score_dosage.vcf
inst/extdata/phased_genotype_fields.vcf
inst/extdata/geno_vcf44.vcf
inst/extdata/fixture_ref.fa
inst/extdata/region_union_no_contig.index.tbi
inst/extdata/score_summaries.list
inst/extdata/bcf_scalar_counts.bcf
inst/extdata/roh_gt_only.vcf
inst/extdata/bcf_offset.vcf.gz.tbi
inst/extdata/bcf_literal_contigs.vcf.gz
inst/extdata/range.bam
inst/extdata/bam_scan_single.bam.csi
inst/extdata/liftover_star_swap.chain
inst/extdata/format_string_list.vcf
inst/extdata/liftover_nw_limit_src.fa.fai
inst/extdata/big.bam.csi
inst/extdata/bcf_scan_contigs.full.vcf.gz.index.csi
inst/extdata/bcf_scan_contigs.none.vcf.gz
inst/extdata/liftover_star_swap_dst.fa
inst/extdata/vcf_file.bcf
inst/extdata/nanopore.bam.bai
inst/extdata/fixture_unmapped.sam
inst/extdata/region_names.fa
inst/extdata/geno_calls.bcf.csi
inst/extdata/bam_mismatch.bam
inst/extdata/formatcols.vcf.gz.csi
inst/extdata/geno_format.vcf
inst/extdata/score_summary_mismatch.tsv
inst/extdata/bam_offset.sam.gz
inst/extdata/geno_ps_width.vcf.gz
inst/extdata/bcf_format_type_clash.bcf
inst/extdata/bam_offset.sam.bgz
inst/extdata/bam_offset_gzip.bam
inst/extdata/bam_materialize.sam
inst/extdata/bam_scan_all_unplaced.bam.legacy.csi
inst/extdata/score_summary_log10p.tsv
inst/extdata/bcf_scan_contigs.bcf.csi
inst/extdata/region_union.bcf.csi
inst/extdata/liftover_nw_limit_src.fa
inst/extdata/malformed_bad_pos.vcf
inst/extdata/gtf_named_attributes.gtf.gz
inst/extdata/test_vep_tidy.vcf
inst/extdata/region_names.fa.gz.fai
inst/extdata/bcf_literal_contigs.bcf.csi
inst/extdata/full-fragment-pairs.bam
inst/extdata/score_summary_or.tsv
inst/extdata/bcf_literal_contigs.vcf
inst/extdata/fixture_mixed.bam
inst/extdata/bam_scan_mixed.bam.legacy.csi
inst/extdata/overlapping-pairs.bam
inst/extdata/bam_mismatch.cram.crai
inst/extdata/geno_ps_payload.bcf
inst/extdata/geno_gt_allele.vcf
inst/extdata/liftover_star_refadd_dst.fa.fai
inst/extdata/gff_attrs.gff3
inst/extdata/region_union_no_contig.vcf.gz
inst/extdata/bam_scan_mixed.cram.crai
inst/extdata/faidx_invalid.fa.fai
inst/extdata/liftover_star_refadd.chain
inst/extdata/bam_mismatch.mask.bcf.csi
inst/extdata/geno_ps_number.bcf
inst/extdata/liftover_chr23_alias_src.fa.fai
inst/extdata/bam_mismatch.fa
inst/extdata/geno_ps_type.bcf
inst/extdata/bcf_literal_contigs.bcf
inst/extdata/bam_scan_all_unplaced.bam
inst/extdata/liftover_nw_limit_dst.fa.fai
inst/extdata/roh_repeated_af.tsv.gz.tbi
inst/extdata/fixture_paired.bam.bai
inst/extdata/gff_strict_valid.gff3
inst/extdata/bcf_scalar_counts.vcf.gz
inst/extdata/geno_format.vcf.gz
inst/extdata/region_union.vcf.gz.tbi
inst/extdata/score_summary_rsid.tsv
inst/extdata/score_summary_saige.tsv
inst/extdata/rg.sam
inst/extdata/liftover_star_refadd_dst.fa
inst/extdata/bam_mismatch.mask.bcf
inst/extdata/bam_scan_all_unplaced.bam.csi
inst/extdata/bcf_scan_contigs.empty.vcf.gz.index.tbi
inst/extdata/geno_gt_allele.bcf
inst/extdata/ce.fa
inst/extdata/bed_error_policy.bed
inst/extdata/missing.bed
inst/extdata/score_summary_custom.tsv
inst/extdata/fixture_mixed_min_depth_regions.bed
inst/extdata/bcf_scan_contigs.partial.vcf.gz
inst/extdata/score_summary_na.tsv
inst/extdata/roh_empty.vcf
inst/extdata/fixture_mixed.bam.bai
inst/extdata/roh_repeated.vcf.gz
inst/extdata/bcf_scan_contigs.shifted.vcf.gz
inst/extdata/region_names.fa.gz
inst/extdata/geno_gt_allele.vcf.gz
inst/extdata/bcf_record_ends.tsv
inst/extdata/bam_scan_malformed.sam
inst/extdata/genbank_gene_order.gb
inst/extdata/score_summary_no_snp.tsv
inst/extdata/fastq_truncated.fq
inst/extdata/ovl.bam
inst/extdata/liftover_nw_limit.chain
inst/extdata/faidx_invalid.fa
inst/extdata/gff_named_attributes.gff3.gz
inst/extdata/r1.fq
inst/extdata/bam_scan_empty.bam.legacy.bai
inst/extdata/formatcols.vcf.gz
inst/extdata/ensembl_release_consequences.vcf
inst/extdata/roh_map_chr2.txt
inst/extdata/faidx_invalid.bed
inst/extdata/genotype_ploidy_edge_cases.vcf
inst/extdata/test_vep_snpeff.vcf
inst/extdata/fixture_mixed.cram.crai
inst/extdata/liftover_chr23_alias_src.fa
inst/extdata/bam_scan_single.bam.legacy.bai
inst/extdata/parallel_empty_contigs.vcf
inst/extdata/roh_repeated_af.tsv.gz
inst/extdata/gtf_attrs.gtf
inst/extdata/liftover_repeat_src.fa
inst/extdata/liftover_clip_pad_src.fa
inst/extdata/score_summary_dir/README.md
inst/extdata/score_summary_dir/score_summary_na.tsv.csi
inst/extdata/score_summary_dir/score_summary.tsv
inst/extdata/score_summary_dir/score_summary.tsv.tbi
inst/extdata/score_summary_dir/score_summary_na.tsv
inst/extdata/score_summary_dir/nested.tsv/ignored.txt
inst/extdata/insert_size/edges.cram.crai
inst/extdata/insert_size/edges.cram
inst/extdata/insert_size/empty.bam
inst/extdata/insert_size/unindexed.bam
inst/extdata/insert_size/edges.bam
inst/extdata/insert_size/empty.cram.crai
inst/extdata/insert_size/insert_size_reference.sql
inst/extdata/insert_size/empty.cram
inst/extdata/insert_size/reference.fa.gz
inst/extdata/insert_size/empty.bam.bai
inst/extdata/insert_size/reference.fa.gz.fai
inst/extdata/insert_size/cases.tsv
inst/extdata/insert_size/edges.bam.bai
inst/extdata/insert_size/metrics.tsv
inst/extdata/insert_size/provenance.txt
inst/extdata/insert_size/histograms.tsv
inst/extdata/insert_size/reference.fa.gz.gzi
inst/function_catalog/functions.tsv
inst/function_catalog/functions.md
inst/function_catalog/reference.md
inst/function_catalog/functions.yaml
inst/duckhts_extension/count_error_model.c
inst/duckhts_extension/count_error_sql.c
inst/duckhts_extension/count_mixture_udf.c
inst/duckhts_extension/bam_mismatch_counts.c
inst/duckhts_extension/roh_udf.c
inst/duckhts_extension/somalier_vcf_extract_sql.c
inst/duckhts_extension/kmer_udf.c
inst/duckhts_extension/insert_size_sql.c
inst/duckhts_extension/count_mixture_model.c
inst/duckhts_extension/bam_mate_overlap_counts.c
inst/duckhts_extension/tabix_reader.c
inst/duckhts_extension/munge_udf.c
inst/duckhts_extension/interval_udf.c
inst/duckhts_extension/liftover_udf.c
inst/duckhts_extension/roh_hmm.c
inst/duckhts_extension/seq_reader.c
inst/duckhts_extension/somalier_matched_sql.c
inst/duckhts_extension/somalier.c
inst/duckhts_extension/bcf_genotypes.c
inst/duckhts_extension/cgranges.c
inst/duckhts_extension/region_list.c
inst/duckhts_extension/duckhts_sources.tsv
inst/duckhts_extension/libbigwig_hfile_io.c
inst/duckhts_extension/samtools_idxstats_table.c
inst/duckhts_extension/extension_registration.c
inst/duckhts_extension/wasm_http_hfile.c
inst/duckhts_extension/bcf_field_vector.c
inst/duckhts_extension/hts_meta_reader.c
inst/duckhts_extension/bam_reader.c
inst/duckhts_extension/bed_line.c
inst/duckhts_extension/bgzip.c
inst/duckhts_extension/vep_parser.c
inst/duckhts_extension/bcf_filter_vector.c
inst/duckhts_extension/quality_encoding_reader.c
inst/duckhts_extension/bam_insert_size_counts.c
inst/duckhts_extension/ancestry_sql.c
inst/duckhts_extension/count_mixture_sql.c
inst/duckhts_extension/somalier_find_sites_sql.c
inst/duckhts_extension/reference_cache.c
inst/duckhts_extension/bam_pileup.c
inst/duckhts_extension/genbank_reader.c
inst/duckhts_extension/bigwig_reader.c
inst/duckhts_extension/count_cells.c
inst/duckhts_extension/genbank_core.c
inst/duckhts_extension/count_error_udf.c
inst/duckhts_extension/named_attribute_columns.c
inst/duckhts_extension/somalier_sex_sql.c
inst/duckhts_extension/variantkey_udf.c
inst/duckhts_extension/depth_state_hmm.c
inst/duckhts_extension/bcftools_norm_udf.c
inst/duckhts_extension/roh_sql.c
inst/duckhts_extension/duckhts.c
inst/duckhts_extension/depth_sql.c
inst/duckhts_extension/mosdepth_table.c
inst/duckhts_extension/bcf_reader.c
inst/duckhts_extension/somalier_sql.c
inst/duckhts_extension/somalier_contamination_sql.c
inst/duckhts_extension/LICENSE
inst/duckhts_extension/geno_reader.c
inst/duckhts_extension/bam_site_counts.c
inst/duckhts_extension/somalier_bam_extract_sql.c
inst/duckhts_extension/bam_bin_counts.c
inst/duckhts_extension/hts_index_builder.c
inst/duckhts_extension/cgranges_api.c
inst/duckhts_extension/depth_state_udf.c
inst/duckhts_extension/bcftools_filter.c
inst/duckhts_extension/bam_bed_coverage.c
inst/duckhts_extension/bcf_scan.c
inst/duckhts_extension/bcf_format.c
inst/duckhts_extension/quality_encoding.c
inst/duckhts_extension/score_udf.c
inst/duckhts_extension/fastq_qc.c
inst/duckhts_extension/roh_sites.c
inst/duckhts_extension/somalier_panel_sql.c
inst/duckhts_extension/include/seq_encoding.h
inst/duckhts_extension/include/bcftools_filter_config.h
inst/duckhts_extension/include/reference_cache.h
inst/duckhts_extension/include/liftover_nw_limit.h
inst/duckhts_extension/include/regions_bind.h
inst/duckhts_extension/include/bed_line.h
inst/duckhts_extension/include/bcf_scan.h
inst/duckhts_extension/include/wasm_socket_compat.h
inst/duckhts_extension/include/bcf_genotypes.h
inst/duckhts_extension/include/count_error_model.h
inst/duckhts_extension/include/cgranges.h
inst/duckhts_extension/include/duckhts_simd_kernels.def
inst/duckhts_extension/include/count_cells.h
inst/duckhts_extension/include/genbank_core.h
inst/duckhts_extension/include/variantkey_compat.h
inst/duckhts_extension/include/region_list.h
inst/duckhts_extension/include/bcf_filter_vector.h
inst/duckhts_extension/include/duckhts_simd.h
inst/duckhts_extension/include/duckhts_somalier_panel_sql.h
inst/duckhts_extension/include/quality_encoding.h
inst/duckhts_extension/include/duckhts_public_macros.h
inst/duckhts_extension/include/depth_state_hmm.h
inst/duckhts_extension/include/duckdb_map.h
inst/duckhts_extension/include/bcftools_shim.h
inst/duckhts_extension/include/bam_site_counts.h
inst/duckhts_extension/include/wasm_http_hfile.h
inst/duckhts_extension/include/bcf_format.h
inst/duckhts_extension/include/duckdb_alloc.h
inst/duckhts_extension/include/duckhts_simd_internal.h
inst/duckhts_extension/include/hts_io_tuning.h
inst/duckhts_extension/include/named_attribute_columns.h
inst/duckhts_extension/include/duckhts_cigar.h
inst/duckhts_extension/include/vep_parser.h
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inst/duckhts_extension/htslib/cram/cram_samtools.h
inst/duckhts_extension/htslib/cram/open_trace_file.c
inst/duckhts_extension/htslib/cram/open_trace_file.h
inst/duckhts_extension/htslib/os/lzma_stub.h
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inst/duckhts_extension/htslib/samples/qtask_unordered.c
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inst/duckhts_extension/htslib/samples/pileup.c
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inst/duckhts_extension/htslib/samples/mod_aux.c
inst/duckhts_extension/htslib/samples/Makefile
inst/duckhts_extension/htslib/htslib/hfile.h
inst/duckhts_extension/htslib/htslib/faidx.h
inst/duckhts_extension/htslib/htslib/synced_bcf_reader.h
inst/duckhts_extension/htslib/htslib/kstring.h
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inst/duckhts_extension/htslib/htslib/kfunc.h
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inst/duckhts_extension/htslib/htslib/khash_str2int.h
inst/duckhts_extension/htslib/htslib/cram.h
inst/duckhts_extension/htslib/htslib/ksort.h
inst/duckhts_extension/htslib/htslib/kroundup.h
inst/duckhts_extension/htslib/htslib/hts_endian.h
inst/duckhts_extension/htslib/htslib/knetfile.h
inst/duckhts_extension/htslib/htslib/hts.h
inst/duckhts_extension/htslib/htslib/bgzf.h
inst/duckhts_extension/htslib/htslib/tbx.h
inst/duckhts_extension/htslib/htslib/hts_alloc.h
inst/duckhts_extension/htslib/htslib/vcf.h
inst/duckhts_extension/htslib/htslib/sam.h
inst/duckhts_extension/htslib/htslib/khash.h
inst/duckhts_extension/htslib/htslib/vcfutils.h
inst/duckhts_extension/htslib/htslib/regidx.h
inst/duckhts_extension/htslib/htslib/klist.h
inst/duckhts_extension/htslib/htslib/hts_log.h
inst/duckhts_extension/htslib/htslib/vcf_sweep.h
inst/duckhts_extension/htslib/htslib/kseq.h
inst/duckhts_extension/htslib/htslib/kbitset.h
inst/duckhts_extension/duckdb_capi/duckdb_extension.h
inst/duckhts_extension/duckdb_capi/LICENSE
inst/duckhts_extension/duckdb_capi/duckdb.h
inst/patches/duckdb_capi_strict_prototypes.patch
inst/tinytest/test_seq_ops.R
inst/tinytest/test_indexes_bgzip.R
inst/tinytest/test_somalier_find_sites.R
inst/tinytest/test_somalier_extraction.R
inst/tinytest/test_sql_quoting.R
inst/tinytest/test_database_lifetime.R
inst/tinytest/test_multi.R
inst/tinytest/test_pileup.R
inst/tinytest/test_munge.R
inst/tinytest/test_bam_scan.R
inst/tinytest/test_basic.R
inst/tinytest/test_score.R
inst/tinytest/test_intervals.R
inst/tinytest/test_genbank.R
inst/tinytest/test_parallel_empty_contigs.R
inst/tinytest/test_bigwig.R
inst/tinytest/test_depth_fraction.R
inst/tinytest/test_quality_encoding.R
inst/tinytest/test_macro_installation.R
inst/tinytest/test_bam_bed_coverage.R
inst/tinytest/test_integration.R
inst/tinytest/test_liftover.R
inst/tinytest/test_bam_mismatch_counts.R
inst/tinytest/test_geno_sites.R
inst/tinytest/test_bam_materialize.R
inst/tinytest/test_ancestry_contracts.R
inst/tinytest/test_convert_parquet.R
inst/tinytest/test_table_overwrite_failure.R
inst/tinytest/test_gxf_named_attributes.R
inst/tinytest/test_bam_file_offset.R
inst/tinytest/test_bcftools_norm.R
inst/tinytest/test_bam_mate_overlap_counts.R
inst/tinytest/test_native_marker.R
inst/tinytest/test_connection.R
inst/tinytest/test_somalier_sex.R
inst/tinytest/test_cigar_utils.R
inst/tinytest/test_samtools_idxstats.R
inst/tinytest/test_cgranges_api.R
inst/tinytest/test_fastq_qc.R
inst/tinytest/test_count_error_fit.R
inst/tinytest/test_bcf_file_offset.R
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inst/tinytest/test_htslib_contract.R
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inst/tinytest/test_geno.R
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inst/tinytest/bcf_snapshot_query.R
inst/tinytest/test_reference_cache.R
inst/tinytest/test_bcf.R
inst/tinytest/test_somalier.R
inst/tinytest/test_region_lists.R
inst/tinytest/test_munge_threading.R
inst/tinytest/test_roh.R
inst/tinytest/test_count_mixture_lowpass.R
inst/tinytest/test_insert_size.R
inst/tinytest/test_liftover_stress.R
inst/tinytest/test_ancestry.R
tests/tinytest.R
tools/append_extension_metadata.R
tools/write_htslib_config.R
tools/bootstrap.R
man/rduckhts_bcf_multi.Rd
man/rduckhts_somalier_vcf_counts.Rd
man/rduckhts_somalier_find_sites.Rd
man/Rduckhts.Rd
man/duckhts_build.Rd
man/rduckhts_pileup.Rd
man/rduckhts_bed_multi.Rd
man/detect_complex_types.Rd
man/rduckhts_bam.Rd
man/rduckhts_geno_sites.Rd
man/rduckhts_htslib_info.Rd
man/rduckhts_roh_counts.Rd
man/rduckhts_fastq.Rd
man/rduckhts_fasta_multi.Rd
man/rduckhts_bam_convert_parquet.Rd
man/rduckhts_depth_region_fraction.Rd
man/rduckhts_bam_multi.Rd
man/rduckhts_ancestry_proportions.Rd
man/rduckhts_fasta.Rd
man/rduckhts_bcftools_norm.Rd
man/rduckhts_htslib_config.Rd
man/rduckhts_genbank.Rd
man/rduckhts_ancestry_bam.Rd
man/extract_map_data.Rd
man/rduckhts_score.Rd
man/rduckhts_somalier_import_sites.Rd
man/rduckhts_simd_backend.Rd
man/duckhts_bootstrap.Rd
man/rduckhts_hts_index_spans.Rd
man/rduckhts_bam_mate_overlap_counts.Rd
man/rduckhts_ancestry_panel.Rd
man/rduckhts_bcf_samples.Rd
man/rduckhts_samtools_idxstats.Rd
man/rduckhts_tabix_index.Rd
man/rduckhts_install_macros.Rd
man/rduckhts_somalier_sex.Rd
man/rduckhts_somalier_sketches.Rd
man/rduckhts_genbank_to_fasta.Rd
man/rduckhts_bam_bin_counts.Rd
man/rduckhts_bed.Rd
man/rduckhts_somalier_bam_counts.Rd
man/rduckhts_depth_bins.Rd
man/rduckhts_bigwig.Rd
man/rduckhts_gtf_multi.Rd
man/normalize_tabix_types.Rd
man/rduckhts_roh.Rd
man/rduckhts_count_mixture_lowpass.Rd
man/rduckhts_bam_index.Rd
man/rduckhts_functions.Rd
man/rduckhts_depth_state_solutions.Rd
man/rduckhts_hts_index_raw.Rd
man/rduckhts_mosdepth.Rd
man/rduckhts_munge.Rd
man/rduckhts_hts_index.Rd
man/rduckhts_depth_sex_fraction.Rd
man/rduckhts_tabix_multi.Rd
man/rduckhts_somalier_relatedness.Rd
man/rduckhts_somalier_charr.Rd
man/rduckhts_bgzip.Rd
man/rduckhts_bcf_index.Rd
man/rduckhts_gff_multi.Rd
man/rduckhts_gff_convert_parquet.Rd
man/extract_array_element.Rd
man/rduckhts_bgunzip.Rd
man/rduckhts_fasta_nuc.Rd
man/rduckhts_tabix.Rd
man/rduckhts_fasta_index.Rd
man/rduckhts_bcf.Rd
man/duckhts_load.Rd
man/rduckhts_tabix_convert_parquet.Rd
man/rduckhts_count_error_fit.Rd
man/rduckhts_detect_quality_encoding.Rd
man/setup_hts_env.Rd
man/rduckhts_hts_header.Rd
man/rduckhts_bam_insert_size_counts.Rd
man/rduckhts_liftover.Rd
man/rduckhts_fastq_multi.Rd
man/rduckhts_load.Rd
man/rduckhts_bam_bed_coverage.Rd
man/rduckhts_gtf.Rd
man/rduckhts_connect.Rd
man/duckdb_type_mappings.Rd
man/rduckhts_ancestry_geno.Rd
man/rduckhts_bcf_convert_parquet.Rd
man/rduckhts_geno.Rd
man/rduckhts_gff.Rd
man/rduckhts_bam_mismatch_counts.Rd
man/rduckhts_htslib_version.Rd
man/rduckhts_somalier_matched_contamination.Rd
