Index

_

__call__() (GenomeDNA method) (GenomeTrack method) (ProgressPercentage method) __getitem__() (AlignmentMatchTable method) (AlignmentTable method) (CdsTable method) (ExonTable method) (GeneTable method) (IntronTable method) (JunctionReadAlignments method) (JunctionReadAlignmentsTable method) (JunctionReadDistribution method) (JunctionReadDistributionTable method) (JunctionTable method) (TranscriptTable method) (VariantTable method) (VCFTable method) __getstate__() (Cds method) (Exon method) (Gene method) (Intron method) (Transcript method) (Variant method) __init__() (Alignment method) (AlignmentMatch method) (Cds method) (DataManager method) (DefaultDataManager method) (Exon method) (GCSDataManager method) (Gene method) (Genome method) (GenomeTrack method) (GenomeTrackBuilder method) (Interval method) (Intron method) (JReadAlignments method) (Junction method) (JunctionReadAlignments method) (JunctionReadDistribution method) (ProgressPercentage method) (ReadAlignments method) (ReadDistributions method) (Transcript method) (Variant method) (VariantGenome method) (VCFTable method) (VCFVariant method)

__len__() (VCFTable method) __new__() (Genome static method) __reduce__() (Genome method) __repr__() (Alignment method) (AlignmentMatch method) (AlignmentMatchTable method) (AlignmentTable method) (Cds method) (CdsTable method) (Exon method) (ExonTable method) (Gene method) (GeneTable method) (Genome method) (GenomeAnnotation method) (GenomeDNA method) (GenomeTrack method) (GenomeTrackBuilder method) (Interval method) (Intron method) (IntronTable method) (JReadAlignments method) (Junction method) (JunctionReadAlignment method) (JunctionReadAlignments method) (JunctionReadAlignmentsTable method) (JunctionReadCount method) (JunctionReadDistribution method) (JunctionReadDistributionTable method) (JunctionTable method) (ReadAlignments method) (ReadDistributions method) (Transcript method) (TranscriptTable method) (Variant method) (VariantGenome method) (VariantTable method) (VCFTable method) (VCFVariant method) __str__() (Interval method) (Variant method) (VCFVariant method) __weakref__ (DataManager attribute) (Genome attribute) (ProgressPercentage attribute)

A

Alignment (class in genome_kit) AlignmentMatch (class in genome_kit) AlignmentMatchTable (class in genome_kit) alignments (Junction property) (ReadAlignments property) AlignmentTable (class in genome_kit) alt (Variant property) anchor (Interval property) anchor_offset (Interval property) annotation (Genome property) apply_variants() (in module genome_kit._apply_variants)

appris_principality() (Genome method) appris_transcripts() (Genome method) as_dna0() (Interval method) as_dna1() (Interval method) as_negative_strand() (Interval method) as_opposite_strand() (Interval method) as_positive_strand() (Interval method) as_rna1() (Interval method) as_ucsc() (Interval method) as_variant_string() (Variant method) (VCFVariant method)

B

binary_version() (GenomeAnnotation static method) build_gencode() (GenomeAnnotation static method) build_jralign() (JReadAlignments static method) build_ncbi_refseq() (GenomeAnnotation static method)

build_ralign() (ReadAlignments static method) build_rdist() (ReadDistributions static method) build_ucsc_refseq() (GenomeAnnotation static method) build_vcfbin() (VCFTable static method)

C

ccds_id (Transcript property) Cds (class in genome_kit) cds (Exon property) cdss (Genome property) (GenomeAnnotation property) (Transcript property) CdsTable (class in genome_kit) chromosome (Interval property) chromosome_size() (Genome method)

chromosomes (Genome property) close() (GenomeTrack method) (JReadAlignments method) (ReadAlignments method) (ReadDistributions method) (VCFTable method) config (Genome property) contains() (Interval method) count (JunctionReadCount property)

D

data_dir (Genome property) data_size (GenomeTrackBuilder property) DataManager (class in genome_kit) DefaultDataManager (class in genome_kit) dim (GenomeTrack property) (GenomeTrackBuilder property)

distance() (Interval method) dna() (Genome method) (VariantGenome method) dnstream_of() (Interval method) dtype (GenomeTrack property) (GenomeTrackBuilder property)

E

end (Interval property) end3 (Interval property) end5 (Interval property) etype (GenomeTrack property) (GenomeTrackBuilder property) exon (Cds property)

Exon (class in genome_kit) exons (Genome property) (GenomeAnnotation property) (Transcript property) ExonTable (class in genome_kit) expand() (Interval method)

F

filename (GenomeAnnotation property) (GenomeDNA property) (GenomeTrack property) (GenomeTrackBuilder property) (JReadAlignments property) (ReadAlignments property) (ReadDistributions property) (VCFTable property) finalize() (GenomeTrackBuilder method) find_3p_aligned() (AlignmentMatchTable method) (AlignmentTable method) (CdsTable method) (ExonTable method) (GeneTable method) (IntronTable method) (JunctionReadAlignmentsTable method) (JunctionReadDistributionTable method) (JunctionTable method) (TranscriptTable method) (VariantTable method) (VCFTable method) find_3p_within() (AlignmentMatchTable method) (AlignmentTable method) (CdsTable method) (ExonTable method) (GeneTable method) (IntronTable method) (JunctionReadAlignmentsTable method) (JunctionReadDistributionTable method) (JunctionTable method) (TranscriptTable method) (VariantTable method) (VCFTable method) find_5p_aligned() (AlignmentMatchTable method) (AlignmentTable method) (CdsTable method) (ExonTable method) (GeneTable method) (IntronTable method) (JunctionReadAlignmentsTable method) (JunctionReadDistributionTable method) (JunctionTable method) (TranscriptTable method) (VariantTable method) (VCFTable method) find_5p_within() (AlignmentMatchTable method) (AlignmentTable method) (CdsTable method) (ExonTable method) (GeneTable method) (IntronTable method) (JunctionReadAlignmentsTable method) (JunctionReadDistributionTable method) (JunctionTable method) (TranscriptTable method) (VariantTable method) (VCFTable method)

find_exact() (AlignmentMatchTable method) (AlignmentTable method) (CdsTable method) (ExonTable method) (GeneTable method) (IntronTable method) (JunctionReadAlignmentsTable method) (JunctionReadDistributionTable method) (JunctionTable method) (TranscriptTable method) (VariantTable method) (VCFTable method) find_motif() (Genome method) (VariantGenome method) find_overlapping() (AlignmentMatchTable method) (AlignmentTable method) (CdsTable method) (ExonTable method) (GeneTable method) (IntronTable method) (JunctionReadAlignmentsTable method) (JunctionReadDistributionTable method) (JunctionTable method) (TranscriptTable method) (VariantTable method) (VCFTable method) find_within() (AlignmentMatchTable method) (AlignmentTable method) (CdsTable method) (ExonTable method) (GeneTable method) (IntronTable method) (JunctionReadAlignmentsTable method) (JunctionReadDistributionTable method) (JunctionTable method) (TranscriptTable method) (VariantTable method) (VCFTable method) first_by_name() (GeneTable method) flush() (GenomeTrackBuilder method) format() (VCFTable method) format_ids (VCFTable property) from_dna0() (Interval static method) from_dna0_coord() (Interval static method) from_dna1() (Interval static method) from_jraligns() (ReadDistributions static method) from_rna1() (Interval static method) from_string() (Variant static method) from_vcf() (VCFTable static method)

G

GCSDataManager (class in genome_kit) Gene (class in genome_kit) gene (Transcript property) genes (Genome property) (GenomeAnnotation property) GeneTable (class in genome_kit) Genome (class in genome_kit) genome_kit.gk_data module GenomeAnnotation (class in genome_kit) GenomeDNA (class in genome_kit) GenomeTrack (class in genome_kit)

GenomeTrackBuilder (class in genome_kit) get_file() (DataManager method) (DefaultDataManager method) (GCSDataManager method) (in module genome_kit.gk_data) GT_HETEROZYGOUS_PHASED_0_1 (VCFTable attribute) GT_HETEROZYGOUS_PHASED_1_0 (VCFTable attribute) GT_HETEROZYGOUS_UNPHASED (VCFTable attribute) GT_HOMOZYGOUS_ALT (VCFTable attribute) GT_HOMOZYGOUS_REF (VCFTable attribute) GT_UNKNOWN (VCFTable attribute) gtrack_version() (GenomeTrack static method)

H

histogram() (GenomeTrack method)

I

id (Exon property) (Gene property) (Transcript property) index (Exon property) (Intron property) index_size (GenomeTrackBuilder property) info() (VCFTable method) info_ids (VCFTable property) intersect() (Interval method) interval (Alignment property) (AlignmentMatch property) (Cds property) Interval (class in genome_kit) interval (Exon property) (Gene property) (Intron property) (Junction property) (JunctionReadAlignments property) (JunctionReadDistribution property) (Transcript property) (Variant property)

interval() (Genome method) intervals() (GenomeTrack method) Intron (class in genome_kit) introns (Genome property) (GenomeAnnotation property) (Transcript property) IntronTable (class in genome_kit) is_positive_strand() (Interval method)

J

jralign_version() (JReadAlignments static method) JReadAlignments (class in genome_kit) Junction (class in genome_kit) JunctionReadAlignment (class in genome_kit) JunctionReadAlignments (class in genome_kit) JunctionReadAlignmentsTable (class in genome_kit)

JunctionReadCount (class in genome_kit) JunctionReadDistribution (class in genome_kit) JunctionReadDistributionTable (class in genome_kit) junctions (JReadAlignments property) (ReadAlignments property) (ReadDistributions property) JunctionTable (class in genome_kit)

L

left (JunctionReadAlignment property) level (Gene property) (Transcript property)

list_available_genomes() (DataManager method) (DefaultDataManager method) (GCSDataManager method)

M

masked() (VCFTable method) matches (Alignment property) (ReadAlignments property) midpoint (Interval property)

mock() (in module genome_kit._cxx_util) mock_result() (in module genome_kit._cxx_util) mock_unreachable() (in module genome_kit._cxx_util) module genome_kit.gk_data

N

name (Gene property) next_cds (Cds property) next_exon (Exon property) (Intron property) next_intron (Exon property) (Intron property)

num_counts (JunctionReadDistribution property) num_reads (JunctionReadAlignments property) (JunctionReadDistribution property) num_samples (VCFTable property) num_variants (JunctionReadAlignment property)

O

overlaps() (Interval method)

P

phase (Cds property) pileup() (ReadAlignments method) position (Variant property) prev_cds (Cds property) prev_exon (Exon property) (Intron property)

prev_intron (Exon property) (Intron property) product (Transcript property) ProgressPercentage (class in genome_kit.data_manager) protein_id (Transcript property)

R

ralign_version() (ReadAlignments static method) rdist_version() (ReadDistributions static method) ReadAlignments (class in genome_kit) ReadDistributions (class in genome_kit) ref (Variant property) reference_genome (Genome property) (GenomeDNA property) (GenomeTrack property) (GenomeTrackBuilder property) (Interval property)

resolution (GenomeTrack property) (GenomeTrackBuilder property) right (JunctionReadAlignment property)

S

sample_names (VCFTable property) sequence_variations() (VCFTable method) set_clamping() (GenomeTrackBuilder method) set_data() (GenomeTrackBuilder method) set_data_from_bed() (GenomeTrackBuilder method) set_data_from_bedgraph() (GenomeTrackBuilder method) set_data_from_wig() (GenomeTrackBuilder method) set_default_value() (GenomeTrackBuilder method) set_dict() (GenomeTrackBuilder method) set_restriction() (GenomeTrackBuilder method) set_sparsity() (GenomeTrackBuilder method) set_transform() (GenomeTrackBuilder method) shift (JunctionReadCount property) shift() (Interval method) spanning() (Interval static method) (Variant static method) start (Interval property) strand (Interval property) (JunctionReadAlignment property) (JunctionReadCount property)

stranded (AlignmentMatchTable property) (AlignmentTable property) (CdsTable property) (ExonTable property) (GeneTable property) (GenomeTrack property) (GenomeTrackBuilder property) (IntronTable property) (JunctionReadAlignmentsTable property) (JunctionReadDistributionTable property) (JunctionTable property) (TranscriptTable property) (VariantTable property) (VCFTable property) strip_mock_bases() (in module genome_kit._cxx_util) subtract() (Interval method) SVTYPE_NA (VCFTable attribute)

T

transcript (Cds property) Transcript (class in genome_kit) transcript (Exon property) (Intron property) transcripts (Gene property) (Genome property) (GenomeAnnotation property)

TranscriptTable (class in genome_kit) tsl (Transcript property) type (Gene property) (Transcript property)

U

upload_file() (DataManager method) (DefaultDataManager method) (GCSDataManager method) (in module genome_kit.gk_data) upstream_of() (Interval method) utr3 (Exon property)

utr3s (Genome property) (GenomeAnnotation property) (Transcript property) utr5 (Exon property) utr5s (Genome property) (GenomeAnnotation property) (Transcript property)

V

Variant (class in genome_kit) variant() (Genome method) variant_dna() (Genome method) VariantGenome (class in genome_kit) variants (AlignmentMatch property) (JReadAlignments property) (ReadAlignments property)

variants() (JunctionReadAlignment method) VariantTable (class in genome_kit) vcfbin_version() (VCFTable static method) VCFTable (class in genome_kit) VCFVariant (class in genome_kit)

W

wget() (in module genome_kit.gk_data) where() (VariantTable method) (VCFTable method)

with_anchor() (Interval method) within() (Interval method) write2bit() (in module genome_kit._twobitutils)