Method List
-
#<< HashTable
-
#<< IntervalList::Set
-
#<< IntervalList::Tree
-
#[] IntervalList::Set
-
[] Codon
-
#[] HashTable::HashLine
-
#[] HashTable
-
[] AminoAcid
-
#[]= HashTable::HashLine
-
#aa Codon
-
aa_for GeneticCode
-
#above? IntervalList::Interval
-
#add IntervalList::TreeNode
-
#add_interval IntervalList
-
#add_line GTF
-
#add_mate Sam
-
#add_tag GO::TagSet
-
alias_key HashTable::HashLine
-
#aliases Codon
-
#alt Mutation
-
#alt Maf::Line
-
#alt_at Mutation
-
#alt_base_quality VCF::Genotype
-
#alt_count Mutation
-
#alt_count VCF::Genotype
-
#alt_freq VCF::Genotype
-
#alt_length VCF::Genotype
-
#alt_map_quality VCF::Genotype
-
#alt_mismatch_count VCF::Genotype
-
#alt_mismatch_rate VCF::Genotype
-
#approve! HashTable::HashLine
-
#approx_depth VCF::Genotype
-
#attr_accessor_of_type DataTypes
-
#attr_array DataTypes
-
#attr_integer DataTypes
-
#attr_string DataTypes
-
#attr_sym DataTypes
-
#barcode TCGA::Sample
-
#below? IntervalList::Interval
-
#best_canonical_txp Oncotator
-
#best_effect_txp Oncotator
-
#breadth_traverse IntervalList::TreeNode
-
build_aa AminoAcid
-
build_codon Codon
-
#build_genotypes VCF::Line
-
#build_introns GTF::Transcript
-
#build_muts VCF::Line
-
#build_tree IntervalList::Tree
-
#build_utrs GTF::Transcript
-
#cache GermDefault
-
#cache_load GermDefault
-
#callable? VCF::Genotype
-
#cancer_type TCGA::Sample
-
#canonical GTF::Gene
-
#canonical_transcript_score GTF::Transcript
-
#cds GTF::Transcript
-
#cds_pos GTF::Transcript
-
#cds_seq GTF::Transcript
-
#cds_size GTF::Transcript
-
#center IntervalList::Interval
-
#centromere Fasta::Chrom
-
#chrom Fasta
-
#chroms Fasta
-
#cigar Sam::Read
-
#clean_header Mutation::Collection
-
#clean_headers Mutation::Collection
-
#clone IntervalList::Interval
-
#codon TriNuc
-
#codons AminoAcid
-
codons_for GeneticCode
-
#collected_terms GO::Term
-
#comment Sam::Header::Record
-
comment HashTable
-
comments Mutation::Collection
-
#compute_degeneracy Codon
-
#concat HashTable
-
#contains? GTF::Transcript
-
#contains? IntervalList::Interval
-
#copy Mutation::Record
-
#copy SegFile::Segment
-
#copy GenomicLocus::Region
-
#copy GTF::Feature
-
#copy GenomicLocus::Position
-
#criteria_failed? Mutation::Filtering
-
#criterion_ok? Mutation::Filtering
-
db_cache Oncotator
-
db_connect Oncotator
-
db_obj Oncotator
-
db_opts Oncotator
-
#def GO::Term
-
#default GermDefault
-
default_create GTF
-
default_sleeve Mutation::Collection
-
#default_stop GenomicLocus
-
#degeneracy Codon
-
delete_key Oncotator
-
#depth VCF::Genotype
-
#depth GO::Term
-
#depth_traverse IntervalList::TreeNode
-
#diff IntervalList::Interval
-
#discard_onco Mutation::Oncotate
-
#dist IntervalList::Interval
-
#distance_to Codon
-
#each IntervalList::Set
-
#each GTF::Gene
-
#each Flagstat
-
#each HashTable
-
#each Sam
-
#each_read Fastq
-
#empty? VCF::Genotype
-
#empty? Oncotator
-
#end_pos Sam::Read
-
#enforce_header VCF
-
#exons GTF::Gene
-
#exons GTF::Transcript
-
#fasta GTF
-
#file_pos Fasta::Chrom
-
#find GO::Ontology
-
find_key Oncotator
-
#first? Sam::Read
-
#flatten IntervalList
-
#format_column VCF::Line
-
#format_column HashTable::HashLine
-
#formatted_header HashTable
-
#gene GTF
-
#gene_annotations GO::Annotation
-
#gene_exp TCGA::RsemExpression
-
#gene_file TCGA::RsemExpression
-
#gene_name Maf::Line
-
#genome_size Fasta
-
#genotype VCF::Line
-
get_conf GermConfig
-
#get_json_object Oncotator
-
#get_key GermConfig
-
#get_masked_seq Fasta
-
#get_nmer_freq FastaAux
-
#get_read Fastq
-
#get_seq Fasta
-
#get_seq_chunk FastaAux
-
#get_seq_starts FastaAux
-
guess_line_size Fasta
-
#has_default GermDefault
-
#header HashTable
-
#header Sam
-
#header GO::Ontology
-
header_off HashTable
-
header_on HashTable
-
#heterozygous? VCF::Genotype
-
#homozygous? VCF::Genotype
-
#id GO::Term
-
#id Fastq::Read
-
#idx HashTable
-
#idx_keys HashTable
-
#in_cosmic Mutation::Oncotate
-
#index TriNuc
-
#initialize HashTable
-
#initialize VCF::Genotype
-
#initialize GermConfig
-
#initialize VCF::Preamble
-
#initialize VCF::Line
-
#initialize SegFile
-
#initialize Fastq
-
#initialize Fastq::Read
-
#initialize AminoAcid
-
#initialize Fasta
-
#initialize Mutation::Collection
-
#initialize Fasta::Chrom
-
#initialize Mutation::Record
-
#initialize TCGA::Sample
-
#initialize TCGA::RsemExpression
-
#initialize IntervalList::TreeNode
-
#initialize Codon
-
#initialize MuTect::Line
-
#initialize GTF::Gene
-
#initialize GTF::Transcript
-
#initialize IntervalList::Set
-
#initialize GenomicLocus::Region
-
#initialize Sam
-
#initialize Mutation
-
#initialize Sam::Read
-
#initialize SDRF
-
#initialize Oncotator::Transcript
-
#initialize Sam::Header::Record
-
#initialize Sam::Header
-
#initialize Oncotator
-
#initialize IntervalList::Tree
-
#initialize Maf::Line
-
#initialize Indelocator
-
#initialize GTF
-
#initialize Indelocator::Line
-
#initialize HashTable::HashLine
-
#initialize GO::Annotation
-
#initialize GO::Ontology
-
#initialize GO::Term
-
#initialize TriNuc
-
#initialize GO::TagSet
-
#initialize Flagstat
-
#initialize GenomicLocus::Position
-
insert_onco Oncotator
-
#inspect GTF::Gene
-
#inspect IntervalList::Set
-
#inspect Fasta
-
#inspect Mutation::Oncotate
-
#inspect Sam
-
#inspect GTF
-
#inspect GO::Ontology
-
#inspect HashTable
-
#inspect GTF::Transcript
-
#intersect IntervalList::Interval
-
#interval_missing? Fasta
-
#interval_set IntervalList
-
#intervals GTF::Gene
-
#intervals GTF::Transcript
-
#intervals_start IntervalList::Tree
-
#intervals_stop IntervalList::Tree
-
#intron_frame GTF::Transcript
-
#intron_pos GTF::Transcript
-
#introns GTF::Transcript
-
#invalid? HashTable::HashLine
-
#invalidate! HashTable::HashLine
-
#is_cancerous Oncotator
-
#is_ccds? GTF::Transcript
-
#is_max? IntervalList::TreeNode
-
#is_snp Oncotator
-
#is_valid? Mutation
-
#junctions Sam::Read
-
#keep_germline? MuTect::Line
-
#keep_germline? Indelocator::Line
-
#keep_somatic? Indelocator::Line
-
#keep_somatic? MuTect::Line
-
#letter AminoAcid
-
#line Sam::Header::Record
-
line_class HashTable
-
#line_size Fasta
-
line_type HashTable
-
#load_centromeres Fasta
-
#load_file HashTableAux
-
#loaded? GermConfig
-
#loc GenomicLocus
-
#locus_seq Fasta
-
#long_chrom GenomicLocus
-
#mapped? Sam::Read
-
#mate Sam::Read
-
#mate_chrom Sam::Read
-
#mate_reversed? Sam::Read
-
#mate_unmapped? Sam::Read
-
#mates Sam
-
#max IntervalList::TreeNode
-
#method_missing GTF::Gene
-
#method_missing Oncotator::Transcript
-
#method_missing GermDefault
-
#method_missing VCF::Genotype
-
#method_missing Maf::Line
-
#method_missing GTF::Feature
-
#method_missing GO::TagSet
-
#method_missing Oncotator
-
#method_missing HashTable::HashLine
-
#method_missing GTF::Transcript
-
#method_missing IntervalList::Tree
-
#method_missing Flagstat
-
might_have Mutation::Collection
-
#mut Mutation::Record
-
#mutation Oncotator
-
#mutation_config Mutation::Collection
-
#muts Mutation::Record
-
#n_depth MuTect::Line
-
#n_depth Indelocator::Line
-
#n_var_freq MuTect::Line
-
#n_var_freq Indelocator::Line
-
#name GTF::Transcript
-
#name GTF::Gene
-
#name AminoAcid
-
#name GO::Term
-
#namespace GO::Term
-
#nearest IntervalList::Tree
-
#nearest IntervalList
-
#nearest IntervalList::TreeNode
-
#onco Mutation::Oncotate
-
#onco_uri Oncotator
-
#ontology GO::Annotation
-
optional Mutation::Collection
-
#other_headers SDRF
-
#output HashTable
-
#output Sam
-
#output Sam::Header
-
#output Sam::Read
-
#overlap IntervalList::TreeNode
-
#overlap IntervalList
-
#overlaps? IntervalList::Interval
-
#p Fasta::Chrom
-
#paired? Sam::Read
-
#parent_terms GO::Term
-
persistent_connection Oncotator
-
#pick_alt VCF::Line
-
#pos GenomicLocus::Position
-
#pos Mutation
-
#pos TriNuc
-
#pph2_class Oncotator
-
#preamble HashTable
-
#preamble Maf
-
#present IntervalList
-
#print Printer
-
#promoters GTF
-
#protein_change GTF::Transcript
-
#protein_seq GTF::Transcript
-
#protein_seq_at GTF::Transcript
-
#q Fasta::Chrom
-
#q0_ratio MuTect::Line
-
#qual Fastq::Read
-
#quality VCF::Genotype
-
#random_chrom Fasta
-
#random_pos Fasta
-
#range GenomicLocus
-
read Sam
-
#reads Sam
-
#records Sam::Header
-
#ref Mutation
-
#ref_at Mutation
-
#ref_count Mutation
-
#ref_count VCF::Genotype
-
#ref_freq VCF::Genotype
-
#ref_length VCF::Genotype
-
#required Mutation::Collection
-
required Mutation::Collection
-
requires Mutation::Collection
-
#respond_to_missing? IntervalList::Tree
-
#respond_to_missing? GTF::Transcript
-
#respond_to_missing? GTF::Gene
-
#respond_to_missing? VCF::Genotype
-
#respond_to_missing? Maf::Line
-
#respond_to_missing? GTF::Feature
-
#respond_to_missing? GO::TagSet
-
#respond_to_missing? HashTable::HashLine
-
#respond_to_missing? Flagstat
-
#reversed? Sam::Read
-
#sample HashTable
-
#samples VCF
-
#sdrf TCGA::RsemExpression
-
#second? Sam::Read
-
#secondary? Sam::Read
-
#select! HashTable
-
#seq TriNuc
-
#seq Fastq::Read
-
#seq GTF::Feature
-
#seq Codon
-
#seq_at Sam::Read
-
#seq_names Fasta
-
#seqname Mutation
-
#seqname GenomicLocus::Region
-
#seqname Fasta::Chrom
-
#seqname GenomicLocus::Position
-
#set_cen_pos Fasta::Chrom
-
#set_table HashTable::HashLine
-
#short AminoAcid
-
#short_chrom GenomicLocus
-
#site GTF::Transcript
-
#site GTF::Gene
-
#size IntervalList::Interval
-
#size Fasta::Chrom
-
#skip_genotype? VCF::Line
-
#skip_oncotator? Mutation::Record
-
#sort_by! HashTable
-
#start GenomicLocus::Region
-
#start Fasta::Chrom
-
#stop Mutation
-
#stop GenomicLocus::Region
-
#strand TriNuc
-
#strand GTF::Gene
-
#sum HashTable
-
#supplementary? Sam::Read
-
#t_depth MuTect::Line
-
#t_depth Indelocator::Line
-
#t_var_freq MuTect::Line
-
#t_var_freq Indelocator::Line
-
#tag GO::TagSet
-
#tags Sam::Header::Record
-
#tags GO::TagSet
-
#term GO::Annotation::AnnotationLine
-
#term GO::Ontology
-
#to_ot Mutation::Oncotate
-
#to_ot Indelocator::Line
-
#to_refflat GTF::Transcript
-
#to_s Mutation
-
#to_s HashTable::HashLine
-
#to_s VCF::Genotype
-
#to_s Sam::Header::Record
-
#total Fasta::Chrom
-
#transcript GTF::Transcript
-
#transcript_start GTF::Transcript
-
#transcripts GTF::Gene
-
#tree IntervalList::Tree
-
#trinucs GTF::Transcript
-
#trinucs_for GTF::Transcript
-
#txp Oncotator
-
#type Sam::Header::Record
-
#types HashTable
-
#unchaste? Sam::Read
-
#unified GTF::Gene
-
#union IntervalList::Interval
-
#unmapped? Sam::Read
-
#update HashTable::HashLine
-
#update_index HashTable
-
#update_max IntervalList::TreeNode
-
#use_header? HashTable
-
use_header? HashTable
-
#utr3 GTF::Transcript
-
#utr5 GTF::Transcript
-
#utr_pos GTF::Transcript
-
#var_freq Mutation
-
#vf_ratio MuTect::Line
-
#wrap HashTable
-
#write Printer