Index

_

__all__ (in module agglovar.pairwise.overlap) __bool__() (agglovar.dev.imports.GlobalImport method) __call__() (agglovar.merge.base.MergeBase method) (agglovar.merge.cumulative.MergeCumulative method) __contains__() (agglovar.bed.col.CoordCol method) (agglovar.pairwise.weights.WeightElement method) (agglovar.pairwise.weights.WeightStrategy method) __delete__() (agglovar.meta.descriptors.AutoInitBase method) __enter__() (agglovar.io.PlainOrGzReader method) __eq__() (agglovar.align.score.AffineScoreModel method) (agglovar.align.score.ScoreModel method) (agglovar.pairwise.weights.WeightColumn method) (agglovar.pairwise.weights.WeightElement method) (agglovar.pairwise.weights.WeightStrategy method) __exit__() (agglovar.io.PlainOrGzReader method) __get__() (agglovar.meta.descriptors.AutoInitBase method) __init_subclass__() (agglovar.meta.descriptors.AutoInitBase class method) __iter__() (agglovar.bed.col.CoordCol method) (agglovar.bed.col.CoordColExpr method) __len__() (agglovar.dev.imports.GlobalImport method) __post_init__() (agglovar.io.PlainOrGzReader method) (agglovar.merge.config.stage.IntersectParamSpec method) (agglovar.seqmatch.MatchScoreModel method) (agglovar.vcf.ContigHeader method) (agglovar.vcf.FormatHeader method) (agglovar.vcf.InfoHeader method) __repr__() (agglovar.align.score.AffineScoreModel method) (agglovar.align.score.ScoreModel method) (agglovar.bed.col.CoordCol method) (agglovar.bed.col.CoordColExpr method) (agglovar.merge.config.stage.IntersectStage method) (agglovar.merge.config.strategy.IntersectStrategy method) (agglovar.pairwise.overlap.PairwiseOverlapStage method) (agglovar.pairwise.weights.WeightColumn method) (agglovar.pairwise.weights.WeightElement method) (agglovar.pairwise.weights.WeightStrategy method) (agglovar.vcf.AltHeader method) (agglovar.vcf.ContigHeader method) (agglovar.vcf.FilterHeader method) (agglovar.vcf.FormatHeader method) (agglovar.vcf.InfoHeader method) (agglovar.vcf.VcfBatch method) (agglovar.vcf.VcfHeader method)

__set__() (agglovar.meta.descriptors.AutoInitBase method) (agglovar.meta.descriptors.BoundedFloat method) (agglovar.meta.descriptors.BoundedInt method) (agglovar.meta.descriptors.CheckedBool method) (agglovar.meta.descriptors.CheckedString method) (agglovar.meta.descriptors.OneWayBool method) __set_name__() (agglovar.meta.descriptors.AutoInitBase method) __slots__ (agglovar.vcf.VcfBatch attribute) __str__() (agglovar.merge.config.strategy.IntersectStrategy method) (agglovar.vcf.AltHeader method) (agglovar.vcf.ContigHeader method) (agglovar.vcf.FilterHeader method) (agglovar.vcf.FormatHeader method) (agglovar.vcf.InfoHeader method) (agglovar.vcf.VcfHeader method)

A

add_alt() (agglovar.vcf.VcfHeader method) add_contig() (agglovar.vcf.VcfHeader method) add_filter() (agglovar.vcf.VcfHeader method) add_format() (agglovar.vcf.VcfHeader method) add_info() (agglovar.vcf.VcfHeader method) add_meta() (agglovar.vcf.VcfHeader method) add_sample() (agglovar.vcf.VcfHeader method) ADV_QRY_ARR (in module agglovar.align.op) ADV_REF_ARR (in module agglovar.align.op) affine_gap (agglovar.seqmatch.MatchScoreModel attribute) AFFINE_SCORE_GAP (in module agglovar.align.score) AFFINE_SCORE_MATCH (in module agglovar.align.score) AFFINE_SCORE_MISMATCH (in module agglovar.align.score) AFFINE_SCORE_TS (in module agglovar.align.score) AffineScoreModel (class in agglovar.align.score) agglovar module agglovar.align module agglovar.align.op module agglovar.align.score module agglovar.bed module agglovar.bed.col module agglovar.bed.intersect module agglovar.bed.join module agglovar.bed.merge module agglovar.dev module agglovar.dev.imports module agglovar.expr module agglovar.expr.variant module agglovar.fa module agglovar.io module agglovar.kmer module agglovar.kmer.plot module agglovar.kmer.util module agglovar.merge module agglovar.merge.base module

agglovar.merge.config module agglovar.merge.config.parser module agglovar.merge.config.stage module agglovar.merge.config.strategy module agglovar.merge.cumulative module agglovar.merge.om module agglovar.meta module agglovar.meta.decorators module agglovar.meta.descriptors module agglovar.pairwise module agglovar.pairwise.base module agglovar.pairwise.overlap module agglovar.pairwise.weights module agglovar.schema module agglovar.seqmatch module agglovar.util module agglovar.util.lazy module agglovar.util.str module agglovar.util.var module agglovar.vcf module alias_to_obj_dict() (in module agglovar.dev.imports) ALIGN_SET (in module agglovar.align.op) allow_match_stage (agglovar.merge.config.stage.IntersectStage attribute) allow_truncation (agglovar.meta.descriptors.BoundedInt attribute) allow_unlimited (agglovar.merge.config.stage.IntersectParamSpec attribute) alt (agglovar.merge.config.stage.IntersectStageDistance attribute) (agglovar.merge.config.stage.IntersectStageExact attribute) AltHeader (class in agglovar.vcf) alts (agglovar.vcf.VcfHeader property) append() (agglovar.kmer.util.KmerUtil method) arg_list (agglovar.merge.config.stage.IntersectStage attribute) as_bool() (in module agglovar.bed.intersect) as_proportion() (in module agglovar.bed.intersect) assembly (agglovar.vcf.ContigHeader attribute) AUTOGEN_COLS (in module agglovar.pairwise.overlap) AutoInitBase (class in agglovar.meta.descriptors)

B

BASE_TO_INT (in module agglovar.kmer.util) BoundedFloat (class in agglovar.meta.descriptors)

BoundedInt (class in agglovar.meta.descriptors) BYTE_SIZE_TO_NUMPY_UINT (in module agglovar.kmer.util)

C

caller_globals (agglovar.dev.imports.GlobalImport attribute) CallsetDefType (in module agglovar.merge.base) canonical_complement() (agglovar.kmer.util.KmerUtil method) check() (agglovar.merge.config.stage.IntersectParamSpec method) check_required_cols() (agglovar.pairwise.base.PairwiseJoin method) check_reserved_cols() (agglovar.pairwise.base.PairwiseJoin method) CheckedBool (class in agglovar.meta.descriptors) CheckedObject (class in agglovar.meta.descriptors) CheckedString (class in agglovar.meta.descriptors) chrom (agglovar.bed.col.CoordCol attribute) (agglovar.bed.col.CoordColExpr attribute) chrom_name (agglovar.bed.col.CoordColExpr property) chunk_range (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) chunk_size (agglovar.pairwise.overlap.PairwiseOverlap attribute) CIGAR_OP_SET (in module agglovar.align.op) cigar_to_arr() (in module agglovar.align.op) clear() (agglovar.dev.imports.GlobalImport method) (agglovar.merge.config.strategy.IntersectStrategy method)

CLIP_SET (in module agglovar.align.op) col (agglovar.pairwise.weights.WeightColumn attribute) col_alt (agglovar.merge.config.stage.IntersectStage attribute) col_names() (agglovar.bed.col.CoordColExpr method) col_ref (agglovar.merge.config.stage.IntersectStage attribute) collision_rename() (in module agglovar.util.str) collision_rename_all() (in module agglovar.util.str) cols (agglovar.pairwise.weights.WeightElement property) columns (agglovar.pairwise.weights.WeightElement attribute) compute_seg_ro (agglovar.pairwise.overlap.PairwiseOverlap attribute) compute_weight (agglovar.pairwise.overlap.PairwiseOverlap attribute) CONSUMES_QRY_ARR (in module agglovar.align.op) CONSUMES_REF_ARR (in module agglovar.align.op) ContigHeader (class in agglovar.vcf) contigs (agglovar.vcf.VcfHeader property) CoordCol (class in agglovar.bed.col) CoordColExpr (class in agglovar.bed.col) cpx (agglovar.vcf.VcfBatch attribute)

D

D (in module agglovar.align.op) default (agglovar.merge.config.stage.IntersectParamSpec attribute) (agglovar.meta.descriptors.AutoInitBase attribute) DEFAULT_ALIGN_SCORE_MODEL (in module agglovar.align.score) DEFAULT_CHUNK_SIZE (in module agglovar.pairwise.overlap) DEFAULT_JOIN_COLS (in module agglovar.pairwise.overlap) default_match_stage (agglovar.merge.config.strategy.IntersectStrategy attribute)

DEFAULT_WEIGHT_STRATEGY (in module agglovar.pairwise.weights) description (agglovar.vcf.AltHeader attribute) (agglovar.vcf.FilterHeader attribute) (agglovar.vcf.FormatHeader attribute) (agglovar.vcf.InfoHeader attribute) dist (agglovar.merge.config.stage.IntersectStageDistance attribute) dotplot() (in module agglovar.kmer.plot) dup (agglovar.vcf.VcfBatch attribute)

E

ElementPriority (class in agglovar.pairwise.weights) elements (agglovar.pairwise.weights.WeightStrategy attribute) end (agglovar.bed.col.CoordCol attribute) (agglovar.bed.col.CoordColExpr attribute) end_name (agglovar.bed.col.CoordColExpr property) EQ (in module agglovar.align.op) equi_join_exprs (agglovar.pairwise.overlap.PairwiseOverlap attribute) EQX_SET (in module agglovar.align.op)

expected_cols (agglovar.pairwise.overlap.PairwiseOverlap attribute) expr (agglovar.pairwise.weights.WeightColumn property) (agglovar.pairwise.weights.WeightElement property) (agglovar.pairwise.weights.WeightStrategy property) EXPR_OFFSET_DIST (in module agglovar.pairwise.overlap) EXPR_OFFSET_PROP (in module agglovar.pairwise.overlap) EXPR_OVERLAP_RO (in module agglovar.pairwise.overlap) EXPR_SZRO (in module agglovar.pairwise.overlap) exprs() (agglovar.bed.col.CoordCol method)

F

fa_info() (in module agglovar.fa) file_date (agglovar.vcf.VcfHeader property) file_path (agglovar.io.PlainOrGzReader attribute) FilterHeader (class in agglovar.vcf) filters (agglovar.vcf.VcfHeader property) find_imports() (in module agglovar.dev.imports)

FIRST (agglovar.merge.cumulative.LeadStrategy attribute) (agglovar.pairwise.weights.ElementPriority attribute) force_end_ro (agglovar.pairwise.overlap.PairwiseOverlap attribute) FormatHeader (class in agglovar.vcf) formats (agglovar.vcf.VcfHeader property) from_definition() (agglovar.pairwise.overlap.PairwiseOverlap class method)

G

gap (agglovar.merge.config.stage.IntersectStageMatch attribute) gap() (agglovar.align.score.AffineScoreModel method) (agglovar.align.score.ScoreModel method) get_affine_by_params() (in module agglovar.align.score) get_coord_cols() (in module agglovar.bed.col)

get_defined_names() (in module agglovar.dev.imports) get_intersect_tuples() (agglovar.merge.base.MergeBase static method) get_matcher() (agglovar.merge.config.stage.IntersectStage method) get_module_definitions() (in module agglovar.dev.imports) get_score_model() (in module agglovar.align.score) GlobalImport (class in agglovar.dev.imports)

H

H (in module agglovar.align.op) has_equi_join (agglovar.pairwise.overlap.PairwiseOverlap property) has_match (agglovar.pairwise.overlap.PairwiseOverlap property) (agglovar.pairwise.overlap.PairwiseOverlapStage property) has_max_val (agglovar.merge.config.stage.IntersectParamSpec property)

has_min_val (agglovar.merge.config.stage.IntersectParamSpec property) has_seg_ro (agglovar.pairwise.overlap.PairwiseOverlap property) (agglovar.pairwise.overlap.PairwiseOverlapStage property) has_vcf_temp (agglovar.merge.config.strategy.IntersectStrategy property) header (agglovar.vcf.VcfBatch attribute)

I

I (in module agglovar.align.op) id_expr (in module agglovar.expr.variant) id_expr_noalias (in module agglovar.expr.variant) id_nonsnv_expr (in module agglovar.expr.variant) id_snv_expr (in module agglovar.expr.variant) id_version_expr() (in module agglovar.util.var) ignored (agglovar.vcf.VcfBatch attribute) immutable() (in module agglovar.meta.decorators) import_stack (agglovar.dev.imports.GlobalImport attribute) info (agglovar.vcf.VcfHeader property) InfoHeader (class in agglovar.vcf) insdel (agglovar.vcf.VcfBatch attribute) INT_STR_SET (in module agglovar.align.op) INT_TO_BASE (in module agglovar.kmer.util) intersect_strategy (agglovar.merge.config.stage.IntersectStage attribute) IntersectConfigLexer (class in agglovar.merge.config.parser)

IntersectConfigParser (class in agglovar.merge.config.parser) IntersectParamSpec (class in agglovar.merge.config.stage) IntersectStage (class in agglovar.merge.config.stage) IntersectStageDistance (class in agglovar.merge.config.stage) IntersectStageExact (class in agglovar.merge.config.stage) IntersectStageMatch (class in agglovar.merge.config.stage) IntersectStageRo (class in agglovar.merge.config.stage) IntersectStrategy (class in agglovar.merge.config.strategy) inv (agglovar.vcf.VcfBatch attribute) INVARIANT_JOIN_COLS (in module agglovar.pairwise.overlap) invert (agglovar.pairwise.weights.WeightColumn attribute) is_any_match (agglovar.merge.config.strategy.IntersectStrategy property) is_equi_offset (agglovar.pairwise.overlap.PairwiseOverlap property) is_gz (agglovar.io.PlainOrGzReader attribute) is_valid (agglovar.vcf.VcfHeader property) iter_vcf() (in module agglovar.vcf)

J

jaccard_kmer (agglovar.seqmatch.MatchScoreModel attribute) join (agglovar.merge.cumulative.MergeCumulative attribute) join() (agglovar.pairwise.base.PairwiseJoin method) JOIN_COL_EXPR (in module agglovar.pairwise.overlap) join_col_exprs (agglovar.pairwise.overlap.PairwiseOverlap attribute)

join_cols (agglovar.pairwise.overlap.PairwiseOverlap attribute) join_filters (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) join_iter() (agglovar.pairwise.base.PairwiseJoin method) (agglovar.pairwise.overlap.PairwiseOverlap method) join_predicates (agglovar.pairwise.overlap.PairwiseOverlapStage attribute)

K

k_bit_size (agglovar.kmer.util.KmerUtil attribute) k_byte_size (agglovar.kmer.util.KmerUtil attribute) k_mask (agglovar.kmer.util.KmerUtil attribute) k_min_mask (agglovar.kmer.util.KmerUtil attribute)

k_min_size (agglovar.kmer.util.KmerUtil attribute) k_size (agglovar.kmer.util.KmerUtil attribute) KmerUtil (class in agglovar.kmer.util) ksize (agglovar.merge.config.stage.IntersectStageMatch attribute)

L

lead_strategy (agglovar.merge.cumulative.MergeCumulative attribute) LeadStrategy (class in agglovar.merge.cumulative) LEFT (agglovar.merge.cumulative.LeadStrategy attribute) length (agglovar.vcf.ContigHeader attribute) lexer (agglovar.merge.config.parser.IntersectConfigLexer attribute) (agglovar.merge.config.parser.IntersectConfigParser attribute)

librl() (in module agglovar.dev.imports) limit (agglovar.merge.config.stage.IntersectStageMatch attribute) list_type (agglovar.merge.config.stage.IntersectParamSpec attribute) literals (agglovar.merge.config.parser.IntersectConfigLexer attribute) lockable() (in module agglovar.meta.decorators)

M

M (in module agglovar.align.op) map_limit (agglovar.seqmatch.MatchScoreModel attribute) match (agglovar.merge.config.stage.IntersectStageMatch attribute) (agglovar.meta.descriptors.CheckedString attribute) (agglovar.seqmatch.MatchScoreModel attribute) match() (agglovar.align.score.AffineScoreModel method) (agglovar.align.score.ScoreModel method) match_alt (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) match_filter_pass (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) match_prop() (agglovar.seqmatch.MatchScoreModel method) match_prop_expr (agglovar.pairwise.overlap.PairwiseOverlap property) match_prop_min (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) match_ref (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) match_score_model (agglovar.pairwise.overlap.PairwiseOverlap attribute) match_stage (agglovar.merge.config.stage.IntersectStage attribute) match_vartype (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) matcher (agglovar.merge.config.stage.IntersectStageMatch attribute) MatchScoreModel (class in agglovar.seqmatch) materialize_pair() (in module agglovar.util.lazy) MAX (agglovar.pairwise.weights.ElementPriority attribute) max_inclusive (agglovar.merge.config.stage.IntersectParamSpec property) (agglovar.meta.descriptors.BoundedFloat attribute) (agglovar.meta.descriptors.BoundedInt attribute) max_len (agglovar.meta.descriptors.CheckedString attribute) max_val (agglovar.merge.config.stage.IntersectParamSpec property) (agglovar.meta.descriptors.BoundedFloat attribute) (agglovar.meta.descriptors.BoundedInt attribute) max_val_tuple (agglovar.merge.config.stage.IntersectParamSpec attribute) max_value (agglovar.pairwise.weights.WeightColumn attribute) max_weight (agglovar.pairwise.weights.WeightElement property) md5 (agglovar.vcf.ContigHeader attribute) merge_depth() (in module agglovar.bed.merge) MergeBase (class in agglovar.merge.base) MergeCumulative (class in agglovar.merge.cumulative) meta (agglovar.vcf.VcfHeader property) min_inclusive (agglovar.merge.config.stage.IntersectParamSpec property) (agglovar.meta.descriptors.BoundedFloat attribute) (agglovar.meta.descriptors.BoundedInt attribute) min_kmer_util (agglovar.kmer.util.KmerUtil attribute) min_len (agglovar.meta.descriptors.CheckedString attribute) min_val (agglovar.merge.config.stage.IntersectParamSpec property) (agglovar.meta.descriptors.BoundedFloat attribute) (agglovar.meta.descriptors.BoundedInt attribute) min_val_tuple (agglovar.merge.config.stage.IntersectParamSpec attribute) min_value (agglovar.pairwise.weights.WeightColumn attribute) min_weight (agglovar.pairwise.weights.WeightElement property) minimizer() (agglovar.kmer.util.KmerUtil method) minimizer_mask (agglovar.kmer.util.KmerUtil attribute) mismatch (agglovar.merge.config.stage.IntersectStageMatch attribute) (agglovar.seqmatch.MatchScoreModel attribute)

mismatch() (agglovar.align.score.AffineScoreModel method) (agglovar.align.score.ScoreModel method) mismatch_model() (agglovar.align.score.AffineScoreModel method) (agglovar.align.score.ScoreModel method) missing (agglovar.pairwise.weights.WeightColumn attribute) (agglovar.pairwise.weights.WeightElement attribute) (agglovar.pairwise.weights.WeightStrategy attribute) mode (agglovar.io.PlainOrGzReader attribute) model_param_string() (agglovar.align.score.AffineScoreModel method) (agglovar.align.score.ScoreModel method) module agglovar agglovar.align agglovar.align.op agglovar.align.score agglovar.bed agglovar.bed.col agglovar.bed.intersect agglovar.bed.join agglovar.bed.merge agglovar.dev agglovar.dev.imports agglovar.expr agglovar.expr.variant agglovar.fa agglovar.io agglovar.kmer agglovar.kmer.plot agglovar.kmer.util agglovar.merge agglovar.merge.base agglovar.merge.config agglovar.merge.config.parser agglovar.merge.config.stage agglovar.merge.config.strategy agglovar.merge.cumulative agglovar.merge.om agglovar.meta agglovar.meta.decorators agglovar.meta.descriptors agglovar.pairwise agglovar.pairwise.base agglovar.pairwise.overlap agglovar.pairwise.weights agglovar.schema agglovar.seqmatch agglovar.util agglovar.util.lazy agglovar.util.str agglovar.util.var agglovar.vcf

N

N (in module agglovar.align.op) n_threads (agglovar.pairwise.overlap.PairwiseOverlap attribute) name (agglovar.merge.config.stage.IntersectParamSpec attribute) name_priv (agglovar.meta.descriptors.AutoInitBase attribute) name_pub (agglovar.meta.descriptors.AutoInitBase attribute) non_optional_default() (agglovar.meta.descriptors.AutoInitBase method) (agglovar.meta.descriptors.BoundedFloat method) (agglovar.meta.descriptors.BoundedInt method) (agglovar.meta.descriptors.CheckedBool method) (agglovar.meta.descriptors.CheckedObject method) (agglovar.meta.descriptors.CheckedString method)

np_int_type (agglovar.kmer.util.KmerUtil attribute) NP_MAX_BIT_SIZE (in module agglovar.kmer.util) NP_MAX_BYTE_SIZE (in module agglovar.kmer.util) NP_MAX_KMER_SIZE (in module agglovar.kmer.util) number (agglovar.vcf.FormatHeader attribute) (agglovar.vcf.InfoHeader attribute)

O

offset_max (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) offset_prop_max (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) OneWayBool (class in agglovar.meta.descriptors)

OP_CHAR (in module agglovar.align.op) OP_CHAR_FUNC (in module agglovar.align.op) OP_CODE (in module agglovar.align.op) optional (agglovar.meta.descriptors.AutoInitBase attribute)

P

P (in module agglovar.align.op) p_error() (agglovar.merge.config.parser.IntersectConfigParser method) p_merge_config() (agglovar.merge.config.parser.IntersectConfigParser method) p_primitive_list_element() (agglovar.merge.config.parser.IntersectConfigParser method) p_primitive_list_elements() (agglovar.merge.config.parser.IntersectConfigParser method) p_spec() (agglovar.merge.config.parser.IntersectConfigParser method) p_spec_list() (agglovar.merge.config.parser.IntersectConfigParser method) p_t_bool() (agglovar.merge.config.parser.IntersectConfigParser method) p_t_float() (agglovar.merge.config.parser.IntersectConfigParser method) p_t_int() (agglovar.merge.config.parser.IntersectConfigParser method) p_t_match() (agglovar.merge.config.parser.IntersectConfigParser method) p_t_primitive_list() (agglovar.merge.config.parser.IntersectConfigParser method) p_t_unlimited() (agglovar.merge.config.parser.IntersectConfigParser method) p_val() (agglovar.merge.config.parser.IntersectConfigParser method) p_val_list() (agglovar.merge.config.parser.IntersectConfigParser method) p_val_primitive() (agglovar.merge.config.parser.IntersectConfigParser method) pairwise_join (agglovar.merge.cumulative.MergeCumulative attribute) pairwise_join() (in module agglovar.bed.join)

pairwise_join_iter() (in module agglovar.bed.join) PairwiseJoin (class in agglovar.pairwise.base) PairwiseOverlap (class in agglovar.pairwise.overlap) PairwiseOverlapStage (class in agglovar.pairwise.overlap) param_spec_list (agglovar.merge.config.stage.IntersectStage attribute) parse() (agglovar.merge.config.parser.IntersectConfigParser method) parse_float() (agglovar.merge.config.parser.IntersectConfigLexer method) parse_int() (agglovar.merge.config.parser.IntersectConfigLexer method) parser (agglovar.merge.config.parser.IntersectConfigParser attribute) PlainOrGzReader (class in agglovar.io) polars_to_vcf_type() (in module agglovar.vcf) pop() (agglovar.dev.imports.GlobalImport method) pos (agglovar.bed.col.CoordCol attribute) (agglovar.bed.col.CoordColExpr attribute) pos_name (agglovar.bed.col.CoordColExpr property) pre_select_filters (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) priority (agglovar.pairwise.weights.WeightStrategy attribute) push() (agglovar.dev.imports.GlobalImport method)

R

range_str (agglovar.meta.descriptors.BoundedFloat property) (agglovar.meta.descriptors.BoundedInt property) read_fai() (in module agglovar.fa) read_seq (agglovar.merge.config.stage.IntersectStage attribute) read_vcf_header() (in module agglovar.vcf) ref (agglovar.merge.config.stage.IntersectStageDistance attribute) (agglovar.merge.config.stage.IntersectStageExact attribute) reference (agglovar.vcf.VcfHeader property) refresh() (agglovar.dev.imports.GlobalImport method) remove_alt() (agglovar.vcf.VcfHeader method) remove_contig() (agglovar.vcf.VcfHeader method) remove_filter() (agglovar.vcf.VcfHeader method)

remove_format() (agglovar.vcf.VcfHeader method) remove_info() (agglovar.vcf.VcfHeader method) remove_sample() (agglovar.vcf.VcfHeader method) required_cols (agglovar.pairwise.base.PairwiseJoin property) (agglovar.pairwise.overlap.PairwiseOverlap property) reserved_cols (agglovar.pairwise.base.PairwiseJoin property) (agglovar.pairwise.overlap.PairwiseOverlap property) RESERVED_COLS (in module agglovar.pairwise.overlap) RESERVED_PARAM_NAMES (in module agglovar.merge.config.stage) rev_complement() (agglovar.kmer.util.KmerUtil method) rev_complement_array() (agglovar.kmer.util.KmerUtil method) ro_min (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) rotate_min (agglovar.seqmatch.MatchScoreModel attribute)

S

S (in module agglovar.align.op) sample_table (agglovar.vcf.VcfBatch attribute) samples (agglovar.vcf.VcfHeader property) score (agglovar.merge.config.stage.IntersectStageMatch attribute) score() (agglovar.align.score.ScoreModel method) score_affine_gap (agglovar.align.score.AffineScoreModel attribute) score_align() (agglovar.seqmatch.MatchScoreModel method) score_align_native() (agglovar.seqmatch.MatchScoreModel method) score_match (agglovar.align.score.AffineScoreModel attribute) score_mismatch (agglovar.align.score.AffineScoreModel attribute) score_model (agglovar.seqmatch.MatchScoreModel attribute) score_operations() (agglovar.align.score.AffineScoreModel method) (agglovar.align.score.ScoreModel method) score_template_switch (agglovar.align.score.AffineScoreModel attribute) ScoreModel (class in agglovar.align.score) seg_ro_min (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) set_config_string() (agglovar.merge.config.strategy.IntersectStrategy method) set_match_stage() (agglovar.merge.config.stage.IntersectStage method) set_strategy_type() (agglovar.merge.config.strategy.IntersectStrategy method)

size_ro_min (agglovar.pairwise.overlap.PairwiseOverlapStage attribute) snv (agglovar.vcf.VcfBatch attribute) sort_cols (in module agglovar.expr.variant) source (agglovar.vcf.InfoHeader attribute) (agglovar.vcf.VcfHeader property) spec_type (agglovar.merge.config.stage.IntersectStage attribute) stage_list (agglovar.merge.config.strategy.IntersectStrategy attribute) stages (agglovar.pairwise.overlap.PairwiseOverlap attribute) STANDARD_FIELDS (in module agglovar.schema) standardize() (in module agglovar.bed.col) strategy_type (agglovar.merge.config.strategy.IntersectStrategy attribute) stream() (in module agglovar.kmer.util) stream_index() (in module agglovar.kmer.util) strip (agglovar.meta.descriptors.CheckedString attribute) sub (agglovar.meta.descriptors.CheckedString attribute) (agglovar.vcf.VcfBatch attribute) sub_per_kmer (agglovar.kmer.util.KmerUtil attribute) szdist (agglovar.merge.config.stage.IntersectStageDistance attribute) szro (agglovar.merge.config.stage.IntersectStageDistance attribute)

T

t_error() (agglovar.merge.config.parser.IntersectConfigLexer method) t_KEYWORD() (agglovar.merge.config.parser.IntersectConfigLexer method) t_KW_FALSE() (agglovar.merge.config.parser.IntersectConfigLexer method) t_KW_MATCH() (agglovar.merge.config.parser.IntersectConfigLexer method) t_KW_TRUE() (agglovar.merge.config.parser.IntersectConfigLexer method) t_T_FLOAT() (agglovar.merge.config.parser.IntersectConfigLexer method) t_T_FLOAT_EXP() (agglovar.merge.config.parser.IntersectConfigLexer method) t_T_INT() (agglovar.merge.config.parser.IntersectConfigLexer method) t_T_INT_MULT() (agglovar.merge.config.parser.IntersectConfigLexer method)

t_T_UNLIMITED() (agglovar.merge.config.parser.IntersectConfigLexer method) template_switch() (agglovar.align.score.AffineScoreModel method) (agglovar.align.score.ScoreModel method) to_kmer() (agglovar.kmer.util.KmerUtil method) to_string() (agglovar.kmer.util.KmerUtil method) tokens (agglovar.merge.config.parser.IntersectConfigLexer attribute) (agglovar.merge.config.parser.IntersectConfigParser attribute) type (agglovar.vcf.FormatHeader attribute) (agglovar.vcf.InfoHeader attribute) TYPE_MATCHER (in module agglovar.merge.config.stage)

U

unlimited_val (agglovar.merge.config.stage.IntersectParamSpec attribute)

url (agglovar.vcf.ContigHeader attribute)

V

val_type (agglovar.merge.config.stage.IntersectParamSpec attribute) validate() (agglovar.meta.descriptors.BoundedFloat method) (agglovar.meta.descriptors.BoundedInt method) (agglovar.meta.descriptors.CheckedString method) validation_errors (agglovar.vcf.VcfHeader property) VAR_ARR (in module agglovar.align.op) VARIANT (in module agglovar.schema) VCF_SAMPLE_FIXED_SCHEMA (in module agglovar.vcf)

VCF_SOURCE (in module agglovar.vcf) vcf_temp (agglovar.merge.config.stage.IntersectStage attribute) VCF_TO_POLARS_TYPE (in module agglovar.vcf) vcf_version (agglovar.vcf.VcfHeader property) VCF_VERSION (in module agglovar.vcf) VcfBatch (class in agglovar.vcf) VcfHeader (class in agglovar.vcf) version (agglovar.vcf.InfoHeader attribute)

W

warn_invalid (agglovar.vcf.VcfHeader property) weight (agglovar.pairwise.weights.WeightColumn attribute) weight_expr (agglovar.pairwise.overlap.PairwiseOverlap property) weight_strategy (agglovar.pairwise.base.PairwiseJoin property)

WeightColumn (class in agglovar.pairwise.weights) WeightElement (class in agglovar.pairwise.weights) WeightStrategy (class in agglovar.pairwise.weights) write_vcf() (in module agglovar.vcf)

X

X (in module agglovar.align.op)