Index

A

add_offset() (supremo_lite.personalize.ChromosomeOffsetTracker method) add_range() (supremo_lite.personalize.FrozenRegionTracker method) add_used_segment() (supremo_lite.personalize.ChromosomeSegmentTracker method) align_bnd_matrices() (supremo_lite.prediction_alignment.PredictionAligner2D method) align_bnd_predictions() (supremo_lite.prediction_alignment.PredictionAligner1D method) align_predictions() (supremo_lite.prediction_alignment.PredictionAligner1D method) (supremo_lite.prediction_alignment.PredictionAligner2D method) align_predictions_by_coordinate() (in module supremo_lite) (in module supremo_lite.prediction_alignment)

all_breakends (supremo_lite.variant_utils.BNDClassifier attribute) alt (supremo_lite.variant_utils.Breakend attribute) (supremo_lite.variant_utils.BreakendVariant attribute) alt_pos (supremo_lite.prediction_alignment.VariantPosition attribute) applied_count (supremo_lite.personalize.VariantApplicator attribute) apply_chromosome_mapping() (in module supremo_lite.chromosome_utils) apply_single_variant_to_window() (supremo_lite.personalize.VariantApplicator method) apply_variants() (supremo_lite.personalize.VariantApplicator method)

B

bin_length (supremo_lite.mock_models.testmodel_1d.TestModel attribute) (supremo_lite.mock_models.testmodel_2d.TestModel2D attribute) bin_size (supremo_lite.prediction_alignment.PredictionAligner1D attribute) (supremo_lite.prediction_alignment.PredictionAligner2D attribute) BNDClassifier (class in supremo_lite.variant_utils) Breakend (class in supremo_lite.variant_utils)

breakend1 (supremo_lite.variant_utils.BreakendPair attribute) breakend2 (supremo_lite.variant_utils.BreakendPair attribute) BreakendPair (class in supremo_lite.variant_utils) BreakendVariant (class in supremo_lite.variant_utils) BRISKET_AVAILABLE (in module supremo_lite) (in module supremo_lite.core)

C

chimeric_sequences (supremo_lite.personalize.ChimericSequenceBuilder attribute) ChimericSequenceBuilder (class in supremo_lite.personalize) chrom (supremo_lite.personalize.VariantApplicator attribute) (supremo_lite.variant_utils.Breakend attribute) (supremo_lite.variant_utils.BreakendVariant attribute) chromosome_offsets (supremo_lite.personalize.ChromosomeOffsetTracker attribute) ChromosomeMismatchError, [1] ChromosomeOffsetTracker (class in supremo_lite.personalize) ChromosomeSegmentTracker (class in supremo_lite.personalize) classification (supremo_lite.variant_utils.Breakend attribute) classify_all_breakends() (supremo_lite.variant_utils.BNDClassifier method) classify_variant_type() (in module supremo_lite) (in module supremo_lite.variant_utils)

contact_matrix_to_vector() (in module supremo_lite.prediction_alignment) coordinate_index (supremo_lite.variant_utils.BNDClassifier attribute) create_breakend_pairs() (in module supremo_lite.variant_utils) create_chromosome_mapping() (in module supremo_lite) (in module supremo_lite.chromosome_utils) create_fusion_from_pair() (supremo_lite.personalize.ChimericSequenceBuilder method) crop_bins (supremo_lite.mock_models.testmodel_1d.TestModel attribute) (supremo_lite.mock_models.testmodel_2d.TestModel2D attribute) crop_length (supremo_lite.mock_models.testmodel_1d.TestModel attribute) (supremo_lite.mock_models.testmodel_2d.TestModel2D attribute) (supremo_lite.prediction_alignment.PredictionAligner1D attribute) (supremo_lite.prediction_alignment.PredictionAligner2D attribute) cumulative_offset (supremo_lite.personalize.VariantApplicator attribute)

D

decode_seq() (in module supremo_lite) (in module supremo_lite.sequence_utils)

diag_offset (supremo_lite.prediction_alignment.PredictionAligner2D attribute)

E

encode_seq() (in module supremo_lite) (in module supremo_lite.sequence_utils)

end_pos (supremo_lite.personalize.SequenceSegment attribute)

F

forward() (supremo_lite.mock_models.testmodel_1d.TestModel method) (supremo_lite.mock_models.testmodel_2d.TestModel2D method)

from_breakend_variant() (supremo_lite.variant_utils.Breakend class method) frozen_tracker (supremo_lite.personalize.VariantApplicator attribute) FrozenRegionTracker (class in supremo_lite.personalize)

G

get_affected_regions() (supremo_lite.variant_utils.BreakendPair method) get_alt_ref_sequences() (in module supremo_lite) (in module supremo_lite.personalize) get_alt_sequences() (in module supremo_lite) (in module supremo_lite.personalize) get_bin_positions() (supremo_lite.prediction_alignment.VariantPosition method) get_chromosome_match_report() (in module supremo_lite.chromosome_utils) get_leftover_sequences() (supremo_lite.personalize.ChromosomeSegmentTracker method) get_offset_at_position() (supremo_lite.personalize.ChromosomeOffsetTracker method) get_pam_disrupting_alt_sequences() (in module supremo_lite) (in module supremo_lite.personalize) get_personal_genome() (in module supremo_lite) (in module supremo_lite.personalize)

get_ref_sequences() (in module supremo_lite) (in module supremo_lite.personalize) get_scrambled_subsequences() (in module supremo_lite) (in module supremo_lite.mutagenesis) get_sequence_segments() (supremo_lite.personalize.ChimericSequenceBuilder method) get_sm_sequences() (in module supremo_lite) (in module supremo_lite.mutagenesis) get_sm_subsequences() (in module supremo_lite) (in module supremo_lite.mutagenesis) get_vcf_chromosomes() (in module supremo_lite) (in module supremo_lite.variant_utils) group_variants_by_semantic_type() (in module supremo_lite.variant_utils)

I

id (supremo_lite.variant_utils.Breakend attribute) (supremo_lite.variant_utils.BreakendVariant attribute) info (supremo_lite.variant_utils.BreakendVariant attribute) inserted_seq (supremo_lite.variant_utils.Breakend attribute) (supremo_lite.variant_utils.BreakendVariant attribute)

intervals (supremo_lite.personalize.FrozenRegionTracker attribute) is_frozen() (supremo_lite.personalize.FrozenRegionTracker method) is_valid (supremo_lite.variant_utils.BreakendPair attribute) IUPAC_CODES (in module supremo_lite.personalize)

L

length (supremo_lite.personalize.SequenceSegment attribute)

load_breakend_variants() (in module supremo_lite.variant_utils)

M

match_chromosomes_with_report() (in module supremo_lite) (in module supremo_lite.chromosome_utils) mate_breakend (supremo_lite.variant_utils.Breakend attribute) mate_chrom (supremo_lite.variant_utils.Breakend attribute) (supremo_lite.variant_utils.BreakendVariant attribute) mate_id (supremo_lite.variant_utils.BreakendVariant attribute) mate_pos (supremo_lite.variant_utils.Breakend attribute) (supremo_lite.variant_utils.BreakendVariant attribute) module supremo_lite supremo_lite.chromosome_utils supremo_lite.core supremo_lite.mock_models supremo_lite.mock_models.testmodel_1d supremo_lite.mock_models.testmodel_2d supremo_lite.mutagenesis supremo_lite.personalize supremo_lite.prediction_alignment supremo_lite.sequence_utils supremo_lite.variant_utils

N

n_final_bins (supremo_lite.mock_models.testmodel_1d.TestModel attribute) (supremo_lite.mock_models.testmodel_2d.TestModel2D attribute) n_initial_bins (supremo_lite.mock_models.testmodel_1d.TestModel attribute) (supremo_lite.mock_models.testmodel_2d.TestModel2D attribute) n_targets (supremo_lite.mock_models.testmodel_1d.TestModel attribute) (supremo_lite.mock_models.testmodel_2d.TestModel2D attribute)

normalize_chromosome_name() (in module supremo_lite) (in module supremo_lite.chromosome_utils) nt_to_1h (in module supremo_lite) (in module supremo_lite.core) nts (in module supremo_lite) (in module supremo_lite.core)

O

offset_tracker (supremo_lite.personalize.VariantApplicator attribute) orientation (supremo_lite.personalize.SequenceSegment attribute) (supremo_lite.variant_utils.Breakend attribute) (supremo_lite.variant_utils.BreakendVariant attribute)

P

parse_breakend_alt() (in module supremo_lite.variant_utils) parse_vcf_info() (in module supremo_lite) (in module supremo_lite.variant_utils)

pos (supremo_lite.variant_utils.Breakend attribute) (supremo_lite.variant_utils.BreakendVariant attribute) PredictionAligner1D (class in supremo_lite.prediction_alignment) PredictionAligner2D (class in supremo_lite.prediction_alignment)

R

rc() (in module supremo_lite) (in module supremo_lite.sequence_utils) rc_str() (in module supremo_lite) (in module supremo_lite.sequence_utils) read_vcf() (in module supremo_lite) (in module supremo_lite.variant_utils) read_vcf_chromosome() (in module supremo_lite) (in module supremo_lite.variant_utils)

read_vcf_chromosomes_chunked() (in module supremo_lite.variant_utils) read_vcf_chunked() (in module supremo_lite) (in module supremo_lite.variant_utils) rearrangement_type (supremo_lite.variant_utils.BreakendPair property) ref (supremo_lite.variant_utils.Breakend attribute) (supremo_lite.variant_utils.BreakendVariant attribute) ref_pos (supremo_lite.prediction_alignment.VariantPosition attribute) ref_sequences (supremo_lite.personalize.ChromosomeSegmentTracker attribute) reference_sequences (supremo_lite.personalize.ChimericSequenceBuilder attribute)

S

seq_length (supremo_lite.mock_models.testmodel_1d.TestModel attribute) (supremo_lite.mock_models.testmodel_2d.TestModel2D attribute) sequence (supremo_lite.personalize.VariantApplicator attribute) sequence_segments (supremo_lite.personalize.ChimericSequenceBuilder attribute) SequenceSegment (class in supremo_lite.personalize) skipped_count (supremo_lite.personalize.VariantApplicator attribute) skipped_variants (supremo_lite.personalize.VariantApplicator attribute) source_chrom (supremo_lite.personalize.SequenceSegment attribute) source_type (supremo_lite.personalize.SequenceSegment attribute) start_pos (supremo_lite.personalize.SequenceSegment attribute) supremo_lite module supremo_lite.chromosome_utils module supremo_lite.core module

supremo_lite.mock_models module supremo_lite.mock_models.testmodel_1d module supremo_lite.mock_models.testmodel_2d module supremo_lite.mutagenesis module supremo_lite.personalize module supremo_lite.prediction_alignment module supremo_lite.sequence_utils module supremo_lite.variant_utils module svlen (supremo_lite.prediction_alignment.VariantPosition attribute)

T

target_size (supremo_lite.prediction_alignment.PredictionAligner1D attribute) (supremo_lite.prediction_alignment.PredictionAligner2D attribute) TestModel (class in supremo_lite.mock_models.testmodel_1d) TestModel2D (class in supremo_lite.mock_models.testmodel_2d) TORCH_AVAILABLE (in module supremo_lite) (in module supremo_lite.core) (in module supremo_lite.mock_models) (in module supremo_lite.mock_models.testmodel_1d) (in module supremo_lite.mock_models.testmodel_2d) (in module supremo_lite.prediction_alignment)

training_step() (supremo_lite.mock_models.testmodel_1d.TestModel method) (supremo_lite.mock_models.testmodel_2d.TestModel2D method) transform_coordinate() (supremo_lite.personalize.ChromosomeOffsetTracker method)

U

used_segments (supremo_lite.personalize.ChromosomeSegmentTracker attribute)

V

validate_breakend_pair() (in module supremo_lite.variant_utils) validate_chromosomes_early() (in module supremo_lite.chromosome_utils) validation_errors (supremo_lite.variant_utils.BreakendPair attribute) validation_warnings (supremo_lite.variant_utils.BreakendPair attribute) variant_type (supremo_lite.prediction_alignment.VariantPosition attribute) (supremo_lite.variant_utils.BreakendVariant attribute)

VariantApplicator (class in supremo_lite.personalize) VariantPosition (class in supremo_lite.prediction_alignment) variants (supremo_lite.personalize.VariantApplicator attribute) vector_to_contact_matrix() (in module supremo_lite.prediction_alignment)