From f8162ba9fb05d9a2af14f05fadb154abb56d1b4f Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Thu, 23 Apr 2026 14:19:07 -0700 Subject: [PATCH 01/11] chore: remove old create_fasta_and_index tool --- divref/divref/tools/create_fasta_and_index.py | 310 ------------------ 1 file changed, 310 deletions(-) delete mode 100644 divref/divref/tools/create_fasta_and_index.py diff --git a/divref/divref/tools/create_fasta_and_index.py b/divref/divref/tools/create_fasta_and_index.py deleted file mode 100644 index 9717ba8..0000000 --- a/divref/divref/tools/create_fasta_and_index.py +++ /dev/null @@ -1,310 +0,0 @@ -"""Tool to build DivRef FASTA sequences and DuckDB index from haplotype Hail tables.""" - -import json -import logging -import os -from pathlib import Path - -import duckdb -import hail as hl -import polars -from fgpyo.io import assert_directory_exists -from fgpyo.io import assert_path_is_readable -from fgpyo.io import assert_path_is_writable - -from divref import defaults -from divref.haplotype import get_haplo_sequence -from divref.haplotype import split_haplotypes - -logger = logging.getLogger(__name__) - - -def build_haplotype_table( - haplotypes_table_path: Path, - gnomad_va_file: Path, - reference_fasta: Path, - window_size: int, - frequency_cutoff: float, - merge: bool, - version_str: str, - reference_genome: str, - tmp_dir: Path, -) -> tuple[hl.Table, list[str]]: - """ - Build the annotated haplotype table with sequences and variant strings. - - Reads the haplotype and gnomAD tables, filters by estimated frequency, optionally - merges single-variant gnomAD sites, assigns sequence IDs, and generates haplotype - sequences with flanking reference context. - - Args: - haplotypes_table_path: Path to the computed haplotypes Hail table. - gnomad_va_file: Path to the gnomAD variant annotations Hail table. - reference_fasta: Path to the reference FASTA. - window_size: Context size for sequence construction and haplotype splitting. - frequency_cutoff: Minimum estimated gnomAD AF for inclusion. - merge: If True, include gnomAD single-variant sites above frequency_cutoff. - version_str: Version identifier for sequence IDs. - reference_genome: Reference genome to use. - tmp_dir: Directory for Hail checkpoint files. - - Returns: - Tuple of (checkpointed Hail table, population legend list). - """ - ht = hl.read_table(str(haplotypes_table_path)).key_by() - va = hl.read_table(str(gnomad_va_file)) - pops_legend: list[str] = va.pops.collect()[0] - - hl.get_reference(reference_genome).add_sequence(str(reference_fasta)) - - logger.info( - "Haplotype table contains %d unique haplotypes above frequency threshold", ht.count() - ) - - count_before = ht.count() - ht = ht.filter(ht.min_variant_frequency > 0) - count_after = ht.count() - if count_after < count_before: - logger.warning( - "Removed %d haplotypes with min_variant_frequency <= 0", count_before - count_after - ) - - fraction_phased = ht.max_empirical_AF / ht.min_variant_frequency - ht = ht.annotate( - fraction_phased=fraction_phased, - estimated_gnomad_AF=hl.min( - ht.gnomad_freqs.map(lambda x: x[ht.max_pop].AF * fraction_phased) - ), - ) - ht = ht.filter(ht.estimated_gnomad_AF >= frequency_cutoff) - ht = split_haplotypes(ht, window_size) - ht = ht.key_by("haplotype").distinct().key_by().drop("haplotype") - ht = ht.annotate( - source="HGDP_haplotype", - all_pop_freqs=ht.all_pop_freqs.map( - lambda x: hl.struct(pop=x.pop, empirical_AC=x.empirical_AC, empirical_AF=x.empirical_AF) - ), - ) - logger.info( - "After splitting at window size %d: %d unique haplotypes above frequency threshold", - window_size, - ht.count(), - ) - - if merge: - va = va.rename({"pop_freqs": "gnomad_freqs"}) - va = va.key_by() - argmax_pop = hl.argmax(va.gnomad_freqs.map(lambda x: hl.max(x.AF))) - va = va.select( - max_pop=argmax_pop, - max_empirical_AF=va.gnomad_freqs[argmax_pop].AF, - fraction_phased=1.0, - estimated_gnomad_AF=va.gnomad_freqs[argmax_pop].AF, - max_empirical_AC=va.gnomad_freqs[argmax_pop].AC, - all_pop_freqs=hl.range(hl.len(va.gnomad_freqs)).map( - lambda i: hl.struct( - pop=i, - empirical_AC=va.gnomad_freqs[i].AC, - empirical_AF=va.gnomad_freqs[i].AF, - ) - ), - source="gnomAD_variant", - variants=[hl.struct(locus=va.locus, alleles=va.alleles)], - gnomad_freqs=[va.gnomad_freqs], - ) - va = va.filter(va.max_empirical_AF >= frequency_cutoff) - ht = ht.union(va, unify=True) - - ht = ht.rename({ - "max_empirical_AF": "popmax_empirical_AF", - "max_empirical_AC": "popmax_empirical_AC", - }) - - ht = ht.add_index() - ht = ht.annotate(sequence=get_haplo_sequence(window_size, ht.variants)) - ht = ht.annotate(variant_strs=ht.variants.map(lambda x: hl.variant_str(x))) - ht = ht.annotate( - sequence_length=hl.len(ht.sequence), - sequence_id=hl.str(f"DR-{version_str}-") + hl.str(ht.idx), - n_variants=hl.len(ht.variants), - ).drop("idx") - - file_suffix = ".haplotypes" if not merge else ".haplotypes_gnomad_merge" - ht = ht.checkpoint(os.path.join(tmp_dir, f"{file_suffix}.ht"), overwrite=True) - - return ht, pops_legend - - -def export_ht_to_dataframe( - ht: hl.Table, - output_base: Path, - file_suffix: str, - pops_legend: list[str], -) -> polars.DataFrame: - """ - Export the haplotype Hail table to a TSV file and return it as a polars DataFrame. - - Args: - ht: Annotated haplotype table with sequences and variant strings. - output_base: Base path for the output TSV file. - file_suffix: Suffix to append before .tsv.bgz (e.g. ".haplotypes"). - pops_legend: Ordered list of population codes for frequency columns. - - Returns: - Polars DataFrame read back from the exported TSV. - """ - out_file_path: str = f"{str(output_base)}{file_suffix}.tsv.bgz" - ht.select( - "sequence", - "sequence_length", - "sequence_id", - "n_variants", - "popmax_empirical_AF", - "popmax_empirical_AC", - "estimated_gnomad_AF", - "fraction_phased", - "source", - max_pop=hl.literal(pops_legend)[ht.max_pop], - variants=hl.delimit(ht.variant_strs, ","), - **{ - f"gnomAD_AF_{pop}": hl.delimit( - ht.gnomad_freqs.map(lambda x, _i=i: hl.format("%.5f", x[_i].AF)), "," - ) - for i, pop in enumerate(pops_legend) - }, - ).export(out_file_path) - - return polars.read_csv( - out_file_path, - separator="\t", - schema_overrides={"sequence_id": polars.String}, - ) - - -def write_fasta_files( - df: polars.DataFrame, - output_base: Path, - file_suffix: str, - split_contigs: bool, -) -> None: - """ - Write FASTA file(s) from the haplotype DataFrame. - - Args: - df: DataFrame with sequence and sequence_id columns. - output_base: Base path for the output FASTA file(s). - file_suffix: Suffix to append before .fasta (e.g. ".haplotypes"). - split_contigs: If True, write one FASTA file per chromosome. - """ - if split_contigs: - df = df.with_columns(contig=df["variants"].str.split(":").list.get(0)) - for chrom in df["contig"].unique().to_list(): - logger.info("Creating FASTA for chromosome %s", chrom) - df2 = df.filter(df["contig"] == chrom) - with open(f"{str(output_base)}{file_suffix}.{chrom}.fasta", "w") as fasta_out: - for sequence, sequence_id in df2.select("sequence", "sequence_id").iter_rows(): - fasta_out.write(f">{sequence_id}\n{sequence}\n") - else: - logger.info("Creating FASTA") - with open(f"{str(output_base)}{file_suffix}.fasta", "w") as fasta_out: - for sequence, sequence_id in df.select("sequence", "sequence_id").iter_rows(): - fasta_out.write(f">{sequence_id}\n{sequence}\n") - - -def create_duckdb_index( - df: polars.DataFrame, # noqa: ARG001 — accessed by DuckDB via SQL `FROM df` - output_base: Path, - file_suffix: str, - window_size: int, - pops_legend: list[str], - version_str: str, -) -> None: - """ - Create a DuckDB index database from the haplotype DataFrame. - - Args: - df: DataFrame with sequence and metadata columns. - output_base: Base path for the output .duckdb file. - file_suffix: Suffix to append before .index.duckdb. - window_size: Window size to store in the index. - pops_legend: Population legend list to store in the index. - version_str: Version string to store in the index. - """ - duckdb_file = f"{str(output_base)}{file_suffix}.index.duckdb" - if os.path.exists(duckdb_file): - os.remove(duckdb_file) - con = duckdb.connect(duckdb_file) - con.execute("CREATE TABLE sequences AS SELECT * FROM df") - con.execute("CREATE INDEX idx_sequence_id ON sequences(sequence_id)") - con.execute("CREATE TABLE window_size AS SELECT ? AS window_size", [window_size]) - con.execute("CREATE TABLE pops_legend AS SELECT ? AS pops_legend", [json.dumps(pops_legend)]) - con.execute("CREATE TABLE VERSION AS SELECT ? AS version", [version_str]) - con.close() - - -def create_fasta_and_index( - *, - haplotypes_table_path: Path, - gnomad_va_file: Path, - reference_fasta: Path, - window_size: int, - output_base: Path, - version_str: str, - merge: bool = False, - frequency_cutoff: float = 0.005, - split_contigs: bool = False, - reference_genome: str = defaults.REFERENCE_GENOME, - tmp_dir: Path = Path("/tmp"), -) -> None: - """ - Convert a haplotype Hail table into FASTA sequences and a searchable DuckDB index. - - Reads the haplotype table, filters by estimated gnomAD allele frequency, optionally - merges in single gnomAD variants, assigns sequence IDs, generates sequence strings - with flanking reference context, and writes FASTA and DuckDB index files for use by - remap_divref. - - Args: - haplotypes_table_path: Path to the Hail table of computed haplotypes - (from compute_haplotypes). - gnomad_va_file: Path to the gnomAD variant annotations Hail table - (from extract_gnomad_afs). - reference_fasta: Path to the reference FASTA for sequence extraction. - window_size: Window size used when generating haplotypes; used as the context - size when constructing sequence strings and stored in the index. - output_base: Base path for output files. Writes {output_base}.haplotypes.tsv.bgz, - {output_base}.haplotypes.fasta (or per-chromosome files), and - {output_base}.haplotypes.index.duckdb. - version_str: Version identifier embedded in sequence IDs (e.g. "1.0"). - merge: If True, include gnomAD single-variant sites above frequency_cutoff. - frequency_cutoff: Minimum estimated gnomAD allele frequency for haplotype inclusion. - split_contigs: If True, write one FASTA file per chromosome. - reference_genome: Reference genome to use. Defaults to "GRCh38". - tmp_dir: Temporary directory for Hail checkpoint files. - """ - assert_directory_exists(haplotypes_table_path) - assert_directory_exists(gnomad_va_file) - assert_path_is_readable(reference_fasta) - assert_path_is_readable(reference_fasta.with_suffix(".fai")) - assert_directory_exists(tmp_dir) - assert_path_is_writable(output_base) - - hl.init(tmp_dir=str(tmp_dir)) - - ht, pops_legend = build_haplotype_table( - haplotypes_table_path=haplotypes_table_path, - gnomad_va_file=gnomad_va_file, - reference_fasta=reference_fasta, - window_size=window_size, - frequency_cutoff=frequency_cutoff, - merge=merge, - version_str=version_str, - reference_genome=reference_genome, - tmp_dir=tmp_dir, - ) - - file_suffix = ".haplotypes" if not merge else ".haplotypes_gnomad_merge" - - df = export_ht_to_dataframe(ht, output_base, file_suffix, pops_legend) - write_fasta_files(df, output_base, file_suffix, split_contigs) - create_duckdb_index(df, output_base, file_suffix, window_size, pops_legend, version_str) From f9c9b5545d49534f6a52591668f537273ba24a60 Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Thu, 23 Apr 2026 14:29:53 -0700 Subject: [PATCH 02/11] feat: add haplotype_coordinates function --- divref/divref/haplotype.py | 28 +++++++++++++++++ divref/tests/test_haplotype.py | 57 ++++++++++++++++++++++++++++++++++ 2 files changed, 85 insertions(+) diff --git a/divref/divref/haplotype.py b/divref/divref/haplotype.py index a704413..27329c4 100644 --- a/divref/divref/haplotype.py +++ b/divref/divref/haplotype.py @@ -158,3 +158,31 @@ def get_range(i: hl.Expression) -> hl.Expression: gnomad_freqs=ht.haplotype_indices.map(lambda i: ht.gnomad_freqs[i]), ) return ht.drop("haplotype_indices") + + +def haplo_coordinates( + window_size: int, + variants: hl.Expression, +) -> hl.Expression: + """ + Compute the 0-based half-open reference genome coordinates of a haplotype sequence window. + + The window spans from `window_size` bases before the first variant to `window_size` bases + after the end of the last variant's reference allele — matching the flanking context added + by get_haplo_sequence. + + Args: + window_size: Number of flanking reference bases on each side (same value passed to + get_haplo_sequence). + variants: Hail array expression of variant structs with locus and alleles fields. + + Returns: + Hail struct expression with int32 fields `start` (inclusive) and `end` (exclusive). + """ + sorted_variants = hl.sorted(variants, key=lambda x: x.locus.position) + min_variant = sorted_variants[0] + max_variant = sorted_variants[-1] + return hl.struct( + start=min_variant.locus.position - window_size, + end=max_variant.locus.position + hl.len(max_variant.alleles[0]) + window_size, + ) diff --git a/divref/tests/test_haplotype.py b/divref/tests/test_haplotype.py index 0238aab..db8ae98 100644 --- a/divref/tests/test_haplotype.py +++ b/divref/tests/test_haplotype.py @@ -8,6 +8,7 @@ import pytest from divref.haplotype import get_haplo_sequence +from divref.haplotype import haplo_coordinates from divref.haplotype import split_haplotypes from divref.haplotype import to_hashable_items from divref.haplotype import variant_distance @@ -232,3 +233,59 @@ def test_split_haplotypes_discards_singleton_segment(hail_context: None) -> None rows = split_haplotypes(ht, window_size=200).collect() assert len(rows) == 1 assert [v.locus.position for v in rows[0].variants] == [500, 501] + + +# --------------------------------------------------------------------------- +# haplo_coordinates +# --------------------------------------------------------------------------- + + +def test_haplo_coordinates_snp(hail_context: None) -> None: # noqa: ARG001 + """Single SNP at position P with window W: start = P - W, end = P + 1 + W.""" + variants = hl.array([_make_variant(100, "A", "T")]) + coords = hl.eval(haplo_coordinates(10, variants)) + assert coords.start == 90 + assert coords.end == 111 + + +def test_haplo_coordinates_insertion(hail_context: None) -> None: # noqa: ARG001 + """Insertion (ref len 1) has the same start/end as a SNP at the same position.""" + variants = hl.array([_make_variant(100, "A", "ACGT")]) + coords = hl.eval(haplo_coordinates(10, variants)) + assert coords.start == 90 + assert coords.end == 111 + + +def test_haplo_coordinates_deletion(hail_context: None) -> None: # noqa: ARG001 + """Deletion with ref len 4 at position 100 with window 10: end = 100 + 4 + 10 = 114.""" + variants = hl.array([_make_variant(100, "ACGT", "A")]) + coords = hl.eval(haplo_coordinates(10, variants)) + assert coords.start == 90 + assert coords.end == 114 + + +def test_haplo_coordinates_multi_variant(hail_context: None) -> None: # noqa: ARG001 + """Start uses first variant; end uses last variant's ref allele end + window.""" + variants = hl.array([ + _make_variant(100, "A", "T"), + _make_variant(200, "GG", "G"), + ]) + coords = hl.eval(haplo_coordinates(10, variants)) + assert coords.start == 90 # 100 - 10 + assert coords.end == 212 # 200 + 2 + 10 + + +def test_haplo_coordinates_matches_sequence_length(hail_context: None) -> None: # noqa: ARG001 + """For a SNP-only haplotype, end - start must equal len(sequence).""" + reference = "0" * 300 + + mock_get_sequence = _create_reference_mock(reference) + + with patch("hail.get_sequence", side_effect=mock_get_sequence): + window = 10 + variants = hl.array([_make_variant(150, "A", "T")]) + seq = hl.eval( + get_haplo_sequence(context_size=window, variants=[_make_variant(150, "A", "T")]) + ) + coords = hl.eval(haplo_coordinates(window, variants)) + assert coords.end - coords.start == len(seq) From ee679912e1e7e81a1417f4516f4291e039962e79 Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Thu, 23 Apr 2026 14:32:40 -0700 Subject: [PATCH 03/11] feat: split create_fasta_and_index into two tools --- divref/divref/main.py | 6 +- divref/divref/tools/create_divref_fasta.py | 51 ++++ divref/divref/tools/create_duckdb_index.py | 329 +++++++++++++++++++++ 3 files changed, 384 insertions(+), 2 deletions(-) create mode 100644 divref/divref/tools/create_divref_fasta.py create mode 100644 divref/divref/tools/create_duckdb_index.py diff --git a/divref/divref/main.py b/divref/divref/main.py index 00a68b7..0f71270 100644 --- a/divref/divref/main.py +++ b/divref/divref/main.py @@ -8,7 +8,8 @@ from divref.tools.compute_haplotype_statistics import compute_haplotype_statistics from divref.tools.compute_haplotypes import compute_haplotypes from divref.tools.compute_variation_ratios import compute_variation_ratios -from divref.tools.create_fasta_and_index import create_fasta_and_index +from divref.tools.create_divref_fasta import create_divref_fasta +from divref.tools.create_duckdb_index import create_duckdb_index from divref.tools.create_gnomad_sites_vcf import create_gnomad_sites_vcf from divref.tools.extract_gnomad_afs import extract_gnomad_afs from divref.tools.extract_gnomad_single_afs import extract_gnomad_single_afs @@ -20,7 +21,8 @@ compute_haplotypes, compute_haplotype_statistics, compute_variation_ratios, - create_fasta_and_index, + create_duckdb_index, + create_divref_fasta, create_gnomad_sites_vcf, extract_gnomad_afs, extract_gnomad_single_afs, diff --git a/divref/divref/tools/create_divref_fasta.py b/divref/divref/tools/create_divref_fasta.py new file mode 100644 index 0000000..898325e --- /dev/null +++ b/divref/divref/tools/create_divref_fasta.py @@ -0,0 +1,51 @@ +"""Tool to write per-chromosome FASTA files from a DivRef DuckDB index.""" + +import logging +from pathlib import Path + +import duckdb +import polars +from fgpyo.io import assert_path_is_readable +from fgpyo.io import assert_path_is_writable + +logger = logging.getLogger(__name__) + + +def _write_fasta_files(df: polars.DataFrame, output_base: Path) -> None: + """ + Write one FASTA file per chromosome to {output_base}.{chrom}.fasta. + + Args: + df: DataFrame with sequence_id, sequence, and variants columns. + output_base: Base path; chromosome name is appended as a suffix. + """ + for chrom in sorted(df["contig"].unique().to_list()): + logger.info("Creating FASTA for chromosome %s", chrom) + df_chrom = df.filter(df["contig"] == chrom) + out_path = Path(f"{output_base}.{chrom}.fasta") + with open(out_path, "w") as fasta_out: + for sequence_id, sequence in df_chrom.select("sequence_id", "sequence").iter_rows(): + fasta_out.write(f">{sequence_id}\n{sequence}\n") + + +def create_divref_fasta( + *, + duckdb_path: Path, + output_base: Path, +) -> None: + """ + Write per-chromosome FASTA files from a DivRef DuckDB index. + + Reads sequence_id, sequence, and variants from the sequences table and writes one FASTA + file per chromosome to {output_base}.{chrom}.fasta. + + Args: + duckdb_path: Path to an existing DivRef DuckDB index. + output_base: Base path for output FASTA files; chromosome name is appended as a suffix. + """ + assert_path_is_readable(duckdb_path) + assert_path_is_writable(output_base) + con = duckdb.connect(str(duckdb_path), read_only=True) + df = con.execute("SELECT sequence_id, sequence, contig FROM sequences").pl() + con.close() + _write_fasta_files(df, output_base) diff --git a/divref/divref/tools/create_duckdb_index.py b/divref/divref/tools/create_duckdb_index.py new file mode 100644 index 0000000..778b370 --- /dev/null +++ b/divref/divref/tools/create_duckdb_index.py @@ -0,0 +1,329 @@ +"""Tool to build DivRef DuckDB index from haplotype Hail tables.""" + +import json +import logging +import os +from pathlib import Path + +import duckdb +import hail as hl +import polars +from fgmetric import Metric +from fgpyo.io import assert_directory_exists +from fgpyo.io import assert_path_is_readable +from fgpyo.io import assert_path_is_writable + +from divref import defaults +from divref.haplotype import get_haplo_sequence +from divref.haplotype import haplo_coordinates +from divref.haplotype import split_haplotypes + +logger = logging.getLogger(__name__) + + +class TablePair(Metric): + """ + Helper class to link a pair of tables for the same contig. + + Attributes: + contig: Contig name. + haplotype_table: HGDP haplotypes Hail table. + sites_table: gnomAD variant Hail table. + """ + + contig: str + haplotype_table_path: Path + sites_table_path: Path + + +def create_duckdb_index( + *, + in_table_pairs_tsv: Path, + reference_fasta: Path, + window_size: int, + output_base: Path, + version: str, + reference_genome: str = defaults.REFERENCE_GENOME, + tmp_dir: Path = Path("/tmp"), +) -> None: + """ + Convert per-chr haplotype and gnomAD variant Hail tables into a searchable DuckDB index. + + Reads and annotates the haplotype and gnomAD variant tables one contig at a time, sorting by + position within each contig. + + Merges all the per-contig tables together, assigns sequence IDs, generates sequence strings with + flanking reference context. + + Writes a DuckDB index file. + + Args: + in_table_pairs_tsv: Path to a TSV file with fields 'contig', 'haplotype_table_path', and + 'sites_table_path'. + reference_fasta: Path to the indexed reference FASTA for sequence extraction. + window_size: Window size used when generating haplotypes; used as the context size when + constructing sequence strings and stored in the index. + output_base: Base path for output files. Writes {output_base}.haplotypes.tsv.bgz and + {output_base}.haplotypes.index.duckdb. + version: Version identifier embedded in sequence IDs (e.g. "1.0"). + reference_genome: Reference genome to use. Defaults to "GRCh38". + tmp_dir: Temporary directory for Hail checkpoint files. + """ + assert_path_is_readable(in_table_pairs_tsv) + assert_path_is_readable(reference_fasta) + assert_path_is_readable(reference_fasta.with_suffix(".fai")) + assert_directory_exists(tmp_dir) + + # fail fast if output files are not writeable + out_table_file: Path = Path(f"{str(output_base)}.haplotypes_gnomad_merge.tsv.bgz") + out_duckdb_file: Path = Path(f"{str(output_base)}.haplotypes_gnomad_merge.index.duckdb") + assert_path_is_writable(out_table_file) + assert_path_is_writable(out_duckdb_file) + + table_pairs: list[TablePair] = list(TablePair.read(in_table_pairs_tsv)) + + # fail fast on input Hail tables + for table_pair in table_pairs: + assert_directory_exists(table_pair.haplotype_table_path) + assert_directory_exists(table_pair.sites_table_path) + + hl.init(tmp_dir=str(tmp_dir)) + + pops_legend: list[str] = hl.read_table(str(table_pairs[0].sites_table_path)).pops.collect()[0] + + ht = build_sequences_table( + table_pairs=table_pairs, + reference_fasta=reference_fasta, + reference_genome=reference_genome, + window_size=window_size, + version=version, + ) + df = export_sequences_table_to_dataframe( + ht=ht, out_file=out_table_file, pops_legend=pops_legend + ) + write_duckdb_index( + df=df, + out_file=out_duckdb_file, + window_size=window_size, + pops_legend=pops_legend, + version=version, + ) + + +def build_hgdp_haplotype_table_entries( + haplotypes_table_path: Path, + window_size: int, +) -> hl.Table: + """ + Build HGDP_haplotype entries for the "sequences" table. + + Reads the haplotype table, splits the haplotypes by window size, and annotates with source and + population frequencies. + + Args: + haplotypes_table_path: Path to the computed haplotypes Hail table. + window_size: Context size for sequence construction and haplotype splitting. + + Returns: + Hail table with added sequences and variant strings. + """ + # Read the table and remove keys + ht = hl.read_table(str(haplotypes_table_path)).key_by() + count_orig: int = ht.count() + logger.info(f"Haplotype table {haplotypes_table_path} contains {count_orig} unique haplotypes.") + + # Split haplotypes by window size + ht = split_haplotypes(ht, window_size) + ht = ht.key_by("haplotype").distinct().key_by().drop("haplotype") + count_after_splitting: int = ht.count() + logger.info( + f"{count_after_splitting} unique haplotypes remaining after splitting at " + f"window size {window_size}" + ) + + # Annotate + ht = ht.annotate( + source="HGDP_haplotype", + all_pop_freqs=ht.all_pop_freqs.map( + lambda x: hl.struct(pop=x.pop, empirical_AC=x.empirical_AC, empirical_AF=x.empirical_AF) + ), + ) + + return ht + + +def build_gnomad_variant_table_entries(sites_table_path: Path) -> hl.Table: + """ + Build gnomAD_variant entries for the "sequences" table. + + Reads the gnomAD table and annotates entries to match the HGDP_haplotype entries. + + Args: + sites_table_path: Path to the gnomAD variant annotations Hail table. + + Returns: + Tuple of (checkpointed Hail table, population legend list). + """ + va = hl.read_table(str(sites_table_path)) + count_orig: int = va.count() + logger.info(f"Variant table {sites_table_path} contains {count_orig} variants.") + + va = va.rename({"pop_freqs": "gnomad_freqs"}) + va = va.key_by() + argmax_pop = hl.argmax(va.gnomad_freqs.map(lambda x: hl.max(x.AF))) + va = va.select( + max_pop=argmax_pop, + max_empirical_AF=va.gnomad_freqs[argmax_pop].AF, + fraction_phased=1.0, + estimated_gnomad_AF=va.gnomad_freqs[argmax_pop].AF, + max_empirical_AC=va.gnomad_freqs[argmax_pop].AC, + all_pop_freqs=hl.range(hl.len(va.gnomad_freqs)).map( + lambda i: hl.struct( + pop=i, + empirical_AC=va.gnomad_freqs[i].AC, + empirical_AF=va.gnomad_freqs[i].AF, + ) + ), + source="gnomAD_variant", + variants=[hl.struct(locus=va.locus, alleles=va.alleles)], + gnomad_freqs=[va.gnomad_freqs], + ) + return va + + +def build_sequences_table( + table_pairs: list[TablePair], + reference_fasta: Path, + reference_genome: str, + window_size: int, + version: str, +) -> hl.Table: + """ + Build the "sequences" table input with sequences and variant strings. + + Prepares and annotates the haplotype and gnomAD tables, assigns sequence IDs, and generates + sequences with flanking reference context. + + Args: + table_pairs: List of table pairs by contig. Sequences will be sorted by reference genome + start position within each contig; contigs will be ordered as input. + reference_fasta: Path to the reference FASTA. + reference_genome: Reference genome to use. + window_size: Context size for sequence construction and haplotype splitting. + version: Version identifier for sequence IDs. + + Returns: + Hail table with sequences, coordinates, and variant strings annotated. + """ + hl.get_reference(reference_genome).add_sequence(str(reference_fasta)) + + sequences_tables: list[hl.Table] = [] + for table_pair in table_pairs: + hgdp_haplotypes_ht: hl.Table = build_hgdp_haplotype_table_entries( + haplotypes_table_path=table_pair.haplotype_table_path, window_size=window_size + ) + gnomad_variants_ht: hl.Table = build_gnomad_variant_table_entries( + sites_table_path=table_pair.sites_table_path + ) + contig_seq_ht: hl.Table = hgdp_haplotypes_ht.union(gnomad_variants_ht) + sequences_tables.append(contig_seq_ht) + + seq_ht: hl.Table = sequences_tables[0].union(*sequences_tables[1:]) + + seq_ht = seq_ht.rename({ + "max_empirical_AF": "popmax_empirical_AF", + "max_empirical_AC": "popmax_empirical_AC", + }) + + seq_ht = seq_ht.annotate( + min_locus=hl.sorted(seq_ht.variants, key=lambda v: v.locus.position)[0].locus + ) + seq_ht = seq_ht.order_by(seq_ht.min_locus).drop("min_locus") + seq_ht = seq_ht.add_index() + coords = haplo_coordinates(window_size, seq_ht.variants) + seq_ht = seq_ht.annotate( + sequence=get_haplo_sequence(window_size, seq_ht.variants), + start=coords.start, + end=coords.end, + ) + seq_ht = seq_ht.annotate(variant_strs=seq_ht.variants.map(lambda x: hl.variant_str(x))) + seq_ht = seq_ht.annotate( + sequence_length=hl.len(seq_ht.sequence), + sequence_id=hl.str(f"DR-{version}-") + hl.str(seq_ht.idx), + n_variants=hl.len(seq_ht.variants), + ).drop("idx") + + return seq_ht + + +def export_sequences_table_to_dataframe( + ht: hl.Table, + out_file: Path, + pops_legend: list[str], +) -> polars.DataFrame: + """ + Export the sequences Hail table to a TSV file and return it as a polars DataFrame. + + Args: + ht: Annotated haplotype/variant table with sequences and variant strings. + out_file: Path for the output TSV file. + pops_legend: Ordered list of population codes for frequency columns. + + Returns: + Polars DataFrame read back from the exported TSV. + """ + ht.select( + "sequence", + "sequence_length", + "sequence_id", + "n_variants", + "start", + "end", + "popmax_empirical_AF", + "popmax_empirical_AC", + "estimated_gnomad_AF", + "fraction_phased", + "source", + max_pop=hl.literal(pops_legend)[ht.max_pop], + variants=hl.delimit(ht.variant_strs, ","), + **{ + f"gnomAD_AF_{pop}": hl.delimit( + ht.gnomad_freqs.map(lambda x, _i=i: hl.format("%.5f", x[_i].AF)), "," + ) + for i, pop in enumerate(pops_legend) + }, + ).export(str(out_file)) + + return polars.read_csv( + out_file, + separator="\t", + schema_overrides={"sequence_id": polars.String}, + ) + + +def write_duckdb_index( + df: polars.DataFrame, # noqa: ARG001 — accessed by DuckDB via SQL `FROM df` + out_file: Path, + window_size: int, + pops_legend: list[str], + version: str, +) -> None: + """ + Create a DuckDB index database from the haplotype DataFrame. + + Args: + df: DataFrame with sequence and metadata columns. + out_file: Path for the output .duckdb file. + window_size: Window size to store in the index. + pops_legend: Population legend list to store in the index. + version: Version string to store in the index. + """ + if os.path.exists(out_file): + os.remove(out_file) + con = duckdb.connect(str(out_file)) + con.execute("CREATE TABLE sequences AS SELECT * FROM df") + con.execute("CREATE INDEX idx_sequence_id ON sequences(sequence_id)") + con.execute("CREATE TABLE window_size AS SELECT ? AS window_size", [window_size]) + con.execute("CREATE TABLE pops_legend AS SELECT ? AS pops_legend", [json.dumps(pops_legend)]) + con.execute("CREATE TABLE VERSION AS SELECT ? AS version", [version]) + con.close() From 8199960b33a094fc8573f46f32f59afdfd0293d5 Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Thu, 23 Apr 2026 14:32:50 -0700 Subject: [PATCH 04/11] feat: add new tools to workflow --- workflows/generate_divref.smk | 76 +++++++++++++++++++++++++++-------- 1 file changed, 60 insertions(+), 16 deletions(-) diff --git a/workflows/generate_divref.smk b/workflows/generate_divref.smk index af6f605..5bf8065 100644 --- a/workflows/generate_divref.smk +++ b/workflows/generate_divref.smk @@ -58,9 +58,9 @@ VCF_EXTS: list[str] = [".vcf.gz", ".vcf.gz.tbi"] rule all: input: - expand(f"{WORK_DIR}/output/hgdp_1kg.haplotypes.{{chrom}}.haplotypes.fasta", chrom=CHROMS), + f"{WORK_DIR}/output/hgdp_1kg.haplotypes_gnomad_merge.index.duckdb", expand( - f"{WORK_DIR}/output/hgdp_1kg.haplotypes.{{chrom}}.haplotypes.index.duckdb", + f"{WORK_DIR}/output/hgdp_1kg.haplotypes_gnomad_merge.{{chrom}}.fasta", chrom=CHROMS, ), @@ -215,36 +215,80 @@ rule index_reference_genome: #################################################################################################### -# Create the DivRef per-chromosome FASTAs and indexes. +# Writes a TSV listing per-chromosome haplotype and gnomAD sites Hail tables for the index builder. #################################################################################################### -rule create_fasta_and_index: +rule create_table_pairs_tsv: input: - haplotypes_ht=f"{WORK_DIR}/haplotypes/hgdp_1kg.haplotypes.{{chrom}}.ht", - variant_ht=f"{WORK_DIR}/inputs/hgdp_1kg.sites.{{chrom}}.ht", + haplotypes_hts=expand( + f"{WORK_DIR}/haplotypes/hgdp_1kg.haplotypes.{{chrom}}.ht", + chrom=CHROMS, + ), + sites_hts=expand( + f"{WORK_DIR}/inputs/hgdp_1kg.sites.{{chrom}}.ht", + chrom=CHROMS, + ), + output: + tsv=f"{WORK_DIR}/inputs/hgdp_1kg.table_pairs.tsv", + run: + with open(output.tsv, "w") as f: + f.write("contig\thaplotype_table_path\tsites_table_path\n") + for chrom in CHROMS: + haplotype_ht = f"{WORK_DIR}/haplotypes/hgdp_1kg.haplotypes.{chrom}.ht" + sites_ht = f"{WORK_DIR}/inputs/hgdp_1kg.sites.{chrom}.ht" + f.write(f"{chrom}\t{haplotype_ht}\t{sites_ht}\n") + + +#################################################################################################### +# Build the DivRef DuckDB index from all per-chromosome haplotype and gnomAD sites Hail tables. +#################################################################################################### +rule create_divref_index: + input: + table_pairs_tsv=f"{WORK_DIR}/inputs/hgdp_1kg.table_pairs.tsv", fasta=f"{WORK_DIR}/inputs/{REFERENCE_GENOME}.fasta", fai=f"{WORK_DIR}/inputs/{REFERENCE_GENOME}.fai", output: - fasta=f"{WORK_DIR}/output/hgdp_1kg.haplotypes.{{chrom}}.haplotypes.fasta", - duckdb_index=f"{WORK_DIR}/output/hgdp_1kg.haplotypes.{{chrom}}.haplotypes.index.duckdb", + duckdb=f"{WORK_DIR}/output/hgdp_1kg.haplotypes_gnomad_merge.index.duckdb", log: - "logs/generate_divref/create_fasta_and_index.{chrom}.log", + "logs/generate_divref/create_divref_index.log", params: window_size=SEQUENCE_WINDOW_SIZE, - output_base=f"{WORK_DIR}/output/hgdp_1kg.haplotypes.{{chrom}}", + output_base=f"{WORK_DIR}/output/hgdp_1kg", version=VERSION, - freq_threshold=HGDP_1KG_MIN_EST_GNOMAD_HAPLOTYPE_AF, tmp_dir=TMP_DIR, shell: """ ( - divref create-fasta-and-index \ - --haplotypes-table-path {input.haplotypes_ht} \ - --gnomad-va-file {input.variant_ht} \ + divref create-duckdb-index \ + --in-table-pairs-tsv {input.table_pairs_tsv} \ --reference-fasta {input.fasta} \ --window-size {params.window_size} \ --output-base {params.output_base} \ - --version-str {params.version} \ - --frequency-cutoff {params.freq_threshold} \ + --version {params.version} \ --tmp-dir {params.tmp_dir} ) &> {log} """ + + +#################################################################################################### +# Write per-chromosome FASTA files from the DivRef DuckDB index. +#################################################################################################### +rule create_divref_fasta: + input: + duckdb=f"{WORK_DIR}/output/hgdp_1kg.haplotypes_gnomad_merge.index.duckdb", + output: + fastas=expand( + f"{WORK_DIR}/output/hgdp_1kg.haplotypes_gnomad_merge.{{chrom}}.fasta", + chrom=CHROMS, + ), + log: + "logs/generate_divref/create_divref_fasta.log", + params: + output_base=f"{WORK_DIR}/output/hgdp_1kg.haplotypes_gnomad_merge", + shell: + """ + ( + divref create-divref-fasta \ + --duckdb-path {input.duckdb} \ + --output-base {params.output_base} + ) &> {log} + """ From f1c0389ce7fd6cfe858de46cb8c6be21dc7f0258 Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Tue, 28 Apr 2026 15:06:48 -0700 Subject: [PATCH 05/11] feat: use unify and specify null --- divref/divref/tools/create_duckdb_index.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/divref/divref/tools/create_duckdb_index.py b/divref/divref/tools/create_duckdb_index.py index 778b370..0082195 100644 --- a/divref/divref/tools/create_duckdb_index.py +++ b/divref/divref/tools/create_duckdb_index.py @@ -225,7 +225,7 @@ def build_sequences_table( gnomad_variants_ht: hl.Table = build_gnomad_variant_table_entries( sites_table_path=table_pair.sites_table_path ) - contig_seq_ht: hl.Table = hgdp_haplotypes_ht.union(gnomad_variants_ht) + contig_seq_ht: hl.Table = hgdp_haplotypes_ht.union(gnomad_variants_ht, unify=True) sequences_tables.append(contig_seq_ht) seq_ht: hl.Table = sequences_tables[0].union(*sequences_tables[1:]) @@ -298,6 +298,7 @@ def export_sequences_table_to_dataframe( out_file, separator="\t", schema_overrides={"sequence_id": polars.String}, + null_values="null", ) From 96f658b9f2e917ae4579a0cd6defe598a6472605 Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Tue, 28 Apr 2026 15:31:05 -0700 Subject: [PATCH 06/11] chore: move pyarrow into pyproject.toml --- divref/pyproject.toml | 1 + divref/uv.lock | 31 + pixi.lock | 2735 ++--------------------------------------- pixi.toml | 1 - 4 files changed, 143 insertions(+), 2625 deletions(-) diff --git a/divref/pyproject.toml b/divref/pyproject.toml index 0146733..5176f02 100644 --- a/divref/pyproject.toml +++ b/divref/pyproject.toml @@ -17,6 +17,7 @@ dependencies = [ "hail>=0.2", "pandas>=2.0", "polars>=1.0", + "pyarrow>=23.0.1,<24", "pydantic>=2.0", "tqdm>=4.0", ] diff --git a/divref/uv.lock b/divref/uv.lock index 56801cd..564eeb9 100644 --- a/divref/uv.lock +++ b/divref/uv.lock @@ -564,6 +564,7 @@ dependencies = [ { name = "hail" }, { name = "pandas" }, { name = "polars" }, + { name = "pyarrow" }, { name = "pydantic" }, { name = "tqdm" }, ] @@ -590,6 +591,7 @@ requires-dist = [ { name = "hail", specifier = ">=0.2" }, { name = "pandas", specifier = ">=2.0" }, { name = "polars", specifier = ">=1.0" }, + { name = "pyarrow", specifier = ">=23.0.1,<24" }, { name = "pydantic", specifier = ">=2.0" }, { name = "tqdm", specifier = ">=4.0" }, ] @@ -1521,6 +1523,35 @@ 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license: Zlib - license_family: Other - purls: [] - size: 95931 - timestamp: 1774072620848 - conda: https://conda.anaconda.org/conda-forge/osx-64/zlib-1.3.2-hbb4bfdb_2.conda sha256: 5dd728cebca2e96fa48d41661f1a35ed0ee3cb722669eee4e2d854c6745655eb md5: 6276aa61ffc361cbf130d78cfb88a237 diff --git a/pixi.toml b/pixi.toml index e60f45e..d34b782 100644 --- a/pixi.toml +++ b/pixi.toml @@ -16,7 +16,6 @@ divref = { path = "./divref", editable = true } snakemake-minimal = ">=8.28.0,<9.0" snakefmt = ">=1.0.0,<2" bcftools = ">=1.23.1,<2" -pyarrow = ">=23.0.1,<24" [feature.analysis.dependencies] r-base = "==4.5.3" From 9e453ec43e421d7452d6c3ecb562ad5726fbf3cd Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Tue, 28 Apr 2026 16:12:39 -0700 Subject: [PATCH 07/11] feat: consolidate frequency filters --- workflows/config/config_schema.yml | 35 ++++++++++-------------------- workflows/generate_divref.smk | 18 +++++---------- 2 files changed, 16 insertions(+), 37 deletions(-) diff --git a/workflows/config/config_schema.yml b/workflows/config/config_schema.yml index b1d8281..7c947f7 100644 --- a/workflows/config/config_schema.yml +++ b/workflows/config/config_schema.yml @@ -53,43 +53,30 @@ properties: description: GCS URI to the HGDP+1KG gnomAD sample metadata Hail table. default: "gs://gcp-public-data--gnomad/release/3.1.2/ht/genomes/gnomad.genomes.v3.1.2.hgdp_1kg_subset_sample_meta.ht" - hgdp_1kg_min_pop_af_extract_gnomad_afs: + hgdp_1kg_min_pop_variant_allele_freq: type: number minimum: 0 maximum: 1 description: | - Minimum allele frequency for at least one selected population when running `divref extract-gnomad-afs`. - Must be <= `hgdp_1kg_min_pop_af_compute_haplotypes`. There are two AF thresholds set in this workflow. - This one is to filter the GCS-hosted Hail table of sites down to a smaller size which is written to - disk for downstream tasks. This step is time-intensive and if we set a relaxed threshold it can be run - once and the outputs re-used for cheaper re-filtering at more stringent thresholds at the `divref - compute-haplotypes` step. - default: 0.001 - - hgdp_1kg_haplotype_window_size: - type: integer - minimum: 1 - description: Window size in bp for grouping variants into haplotypes. - default: 100 - - hgdp_1kg_min_pop_af_compute_haplotypes: - type: number - minimum: 0 - maximum: 1 - description: | - Minimum allele frequency for a variant in at least one selected population when running - `divref compute-haplotypes`. + Minimum variant allele frequency for at least one selected population when running + `divref extract-gnomad-afs` and `divref compute-haplotypes`. Also applied to default: 0.005 - hgdp_1kg_min_estimated_gnomad_haplotype_af: + hgdp_1kg_min_estimated_gnomad_haplotype_allele_freq: type: number minimum: 0 maximum: 1 description: | Minimum estimated gnomAD haplotype allele frequency for inclusion in output. Used by - `divref create-fasta-and-index`. + `divref compute-haplotypes`. default: 0.005 + hgdp_1kg_haplotype_window_size: + type: integer + minimum: 1 + description: Window size in bp for grouping variants into haplotypes. + default: 100 + sequence_window_size: type: integer description: | diff --git a/workflows/generate_divref.smk b/workflows/generate_divref.smk index 5bf8065..e6c312e 100644 --- a/workflows/generate_divref.smk +++ b/workflows/generate_divref.smk @@ -35,20 +35,12 @@ HGDP_1KG_PHASED_BCF_PREFIX: str = config["hgdp_1kg_phased_bcf_prefix"] HGDP_1KG_PHASED_BCF_SUFFIX: str = config["hgdp_1kg_phased_bcf_suffix"] HGDP_1KG_VARIANT_ANNOTATION_HAIL_TABLE: str = config["hgdp_1kg_variant_annotation_hail_table"] HGDP_1KG_SAMPLE_METADATA_HAIL_TABLE: str = config["hgdp_1kg_sample_metadata_hail_table"] -HGDP_1KG_MIN_POP_AF_EXTRACT_GNOMAD_AFS: float = config["hgdp_1kg_min_pop_af_extract_gnomad_afs"] +HGDP_1KG_MIN_POP_VARIANT_AF: float = config["hgdp_1kg_min_pop_variant_allele_freq"] +HGDP_1KG_MIN_POP_HAPLOTYPE_AF: float = config["hgdp_1kg_min_estimated_gnomad_haplotype_allele_freq"] HGDP_1KG_HAPLOTYPE_WINDOW_SIZE: int = config["hgdp_1kg_haplotype_window_size"] -HGDP_1KG_MIN_POP_AF_COMPUTE_HAPLOTYPES: float = config["hgdp_1kg_min_pop_af_compute_haplotypes"] -HGDP_1KG_MIN_EST_GNOMAD_HAPLOTYPE_AF: float = config["hgdp_1kg_min_estimated_gnomad_haplotype_af"] SEQUENCE_WINDOW_SIZE: int = config["sequence_window_size"] -if HGDP_1KG_MIN_POP_AF_EXTRACT_GNOMAD_AFS > HGDP_1KG_MIN_POP_AF_COMPUTE_HAPLOTYPES: - raise ValueError( - f"hgdp_1kg_min_pop_af_extract_gnomad_afs ({HGDP_1KG_MIN_POP_AF_EXTRACT_GNOMAD_AFS}) " - f"must be <= hgdp_1kg_min_pop_af_compute_haplotypes " - f"({HGDP_1KG_MIN_POP_AF_COMPUTE_HAPLOTYPES})" - ) - VCF_EXTS: list[str] = [".vcf.gz", ".vcf.gz.tbi"] #################################################################################################### @@ -104,7 +96,7 @@ rule extract_gnomad_afs: "logs/generate_divref/extract_gnomad_afs.{chrom}.log", params: variant_ht=HGDP_1KG_VARIANT_ANNOTATION_HAIL_TABLE, - freq_threshold=HGDP_1KG_MIN_POP_AF_EXTRACT_GNOMAD_AFS, + freq_threshold=HGDP_1KG_MIN_POP_VARIANT_AF, populations=" ".join(POPS), shell: """ @@ -154,8 +146,8 @@ rule compute_haplotypes: "logs/generate_divref/compute_haplotypes.{chrom}.log", params: window_size=HGDP_1KG_HAPLOTYPE_WINDOW_SIZE, - variant_freq_threshold=HGDP_1KG_MIN_POP_AF_COMPUTE_HAPLOTYPES, - haplotype_freq_threshold=HGDP_1KG_MIN_EST_GNOMAD_HAPLOTYPE_AF, + variant_freq_threshold=HGDP_1KG_MIN_POP_VARIANT_AF, + haplotype_freq_threshold=HGDP_1KG_MIN_POP_HAPLOTYPE_AF, output_base=f"{WORK_DIR}/haplotypes/hgdp_1kg.haplotypes.{{chrom}}", shell: """ From 659ee6ed5c5a6c96d084b3d3c119f30d0a4cb73d Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Tue, 28 Apr 2026 16:13:03 -0700 Subject: [PATCH 08/11] fix: add contig to database, fix schema overrides for population AFs --- divref/divref/tools/create_duckdb_index.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/divref/divref/tools/create_duckdb_index.py b/divref/divref/tools/create_duckdb_index.py index 0082195..00b09f4 100644 --- a/divref/divref/tools/create_duckdb_index.py +++ b/divref/divref/tools/create_duckdb_index.py @@ -243,6 +243,7 @@ def build_sequences_table( coords = haplo_coordinates(window_size, seq_ht.variants) seq_ht = seq_ht.annotate( sequence=get_haplo_sequence(window_size, seq_ht.variants), + contig=seq_ht.variants[0].locus.contig, start=coords.start, end=coords.end, ) @@ -277,6 +278,7 @@ def export_sequences_table_to_dataframe( "sequence_length", "sequence_id", "n_variants", + "contig", "start", "end", "popmax_empirical_AF", @@ -294,10 +296,14 @@ def export_sequences_table_to_dataframe( }, ).export(str(out_file)) + schema_overrides: dict[str, type[polars.DataType]] = { + "sequence_id": polars.String, + **{f"gnomAD_AF_{pop}": polars.String for pop in pops_legend}, + } return polars.read_csv( out_file, separator="\t", - schema_overrides={"sequence_id": polars.String}, + schema_overrides=schema_overrides, null_values="null", ) From 1b6337136227d73bdf068856cb1b87bfe2d49cf9 Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Wed, 29 Apr 2026 09:23:47 -0700 Subject: [PATCH 09/11] chore: fix up docstring in config --- workflows/config/config_schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/config/config_schema.yml b/workflows/config/config_schema.yml index 7c947f7..9b18260 100644 --- a/workflows/config/config_schema.yml +++ b/workflows/config/config_schema.yml @@ -59,7 +59,7 @@ properties: maximum: 1 description: | Minimum variant allele frequency for at least one selected population when running - `divref extract-gnomad-afs` and `divref compute-haplotypes`. Also applied to + `divref extract-gnomad-afs` and `divref compute-haplotypes`. default: 0.005 hgdp_1kg_min_estimated_gnomad_haplotype_allele_freq: From a1c8bda2b849e3da955bf2a208fc43c6dfbb9f2e Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Wed, 29 Apr 2026 09:25:08 -0700 Subject: [PATCH 10/11] fix: argmax calculation --- divref/divref/tools/create_duckdb_index.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/divref/divref/tools/create_duckdb_index.py b/divref/divref/tools/create_duckdb_index.py index 00b09f4..9f33063 100644 --- a/divref/divref/tools/create_duckdb_index.py +++ b/divref/divref/tools/create_duckdb_index.py @@ -170,7 +170,7 @@ def build_gnomad_variant_table_entries(sites_table_path: Path) -> hl.Table: va = va.rename({"pop_freqs": "gnomad_freqs"}) va = va.key_by() - argmax_pop = hl.argmax(va.gnomad_freqs.map(lambda x: hl.max(x.AF))) + argmax_pop = hl.argmax(va.gnomad_freqs.map(lambda x: x.AF)) va = va.select( max_pop=argmax_pop, max_empirical_AF=va.gnomad_freqs[argmax_pop].AF, From 8abb405138e2be8b606ea9eeee2044fe467ffb29 Mon Sep 17 00:00:00 2001 From: Alison Meynert Date: Wed, 29 Apr 2026 09:34:25 -0700 Subject: [PATCH 11/11] feat: fix haplotype coordinates --- divref/divref/haplotype.py | 6 ++++-- divref/tests/test_haplotype.py | 20 ++++++++++---------- 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/divref/divref/haplotype.py b/divref/divref/haplotype.py index 27329c4..93543d9 100644 --- a/divref/divref/haplotype.py +++ b/divref/divref/haplotype.py @@ -167,6 +167,8 @@ def haplo_coordinates( """ Compute the 0-based half-open reference genome coordinates of a haplotype sequence window. + The variant position coordinate is 1-based. + The window spans from `window_size` bases before the first variant to `window_size` bases after the end of the last variant's reference allele — matching the flanking context added by get_haplo_sequence. @@ -183,6 +185,6 @@ def haplo_coordinates( min_variant = sorted_variants[0] max_variant = sorted_variants[-1] return hl.struct( - start=min_variant.locus.position - window_size, - end=max_variant.locus.position + hl.len(max_variant.alleles[0]) + window_size, + start=min_variant.locus.position - 1 - window_size, + end=max_variant.locus.position - 1 + hl.len(max_variant.alleles[0]) + window_size, ) diff --git a/divref/tests/test_haplotype.py b/divref/tests/test_haplotype.py index db8ae98..f473c2d 100644 --- a/divref/tests/test_haplotype.py +++ b/divref/tests/test_haplotype.py @@ -244,35 +244,35 @@ def test_haplo_coordinates_snp(hail_context: None) -> None: # noqa: ARG001 """Single SNP at position P with window W: start = P - W, end = P + 1 + W.""" variants = hl.array([_make_variant(100, "A", "T")]) coords = hl.eval(haplo_coordinates(10, variants)) - assert coords.start == 90 - assert coords.end == 111 + assert coords.start == 89 + assert coords.end == 110 def test_haplo_coordinates_insertion(hail_context: None) -> None: # noqa: ARG001 """Insertion (ref len 1) has the same start/end as a SNP at the same position.""" variants = hl.array([_make_variant(100, "A", "ACGT")]) coords = hl.eval(haplo_coordinates(10, variants)) - assert coords.start == 90 - assert coords.end == 111 + assert coords.start == 89 + assert coords.end == 110 def test_haplo_coordinates_deletion(hail_context: None) -> None: # noqa: ARG001 - """Deletion with ref len 4 at position 100 with window 10: end = 100 + 4 + 10 = 114.""" + """Deletion with ref len 4 at position 100 with window 10: end = 100 - 1 + 4 + 10 = 113.""" variants = hl.array([_make_variant(100, "ACGT", "A")]) coords = hl.eval(haplo_coordinates(10, variants)) - assert coords.start == 90 - assert coords.end == 114 + assert coords.start == 89 + assert coords.end == 113 def test_haplo_coordinates_multi_variant(hail_context: None) -> None: # noqa: ARG001 - """Start uses first variant; end uses last variant's ref allele end + window.""" + """Start uses first variant; end uses last variant + ref allele length + window.""" variants = hl.array([ _make_variant(100, "A", "T"), _make_variant(200, "GG", "G"), ]) coords = hl.eval(haplo_coordinates(10, variants)) - assert coords.start == 90 # 100 - 10 - assert coords.end == 212 # 200 + 2 + 10 + assert coords.start == 89 # 100 - 1 - 10 + assert coords.end == 211 # 200 -1 + 2 + 10 def test_haplo_coordinates_matches_sequence_length(hail_context: None) -> None: # noqa: ARG001