getters.txt

EMBL parser (Kieron):

getSequence
getAccessions
getDescription
getKeywords
getSpecies
getClassification
getRawID
getRawAccessions
getRawDescription
getRawKeywords
getRawDate
getRawSpecies
getRawClassification
getRawReferences
getRawFeatures
getRawComments
getRawAssemblyHeader
getRawAssembly
getRawContig

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TrackBased parser (Anne) - common metadata for the following formats: BED, PSL, WIG

get_browser_switches
get_metadata_value

BED parser (Anne):

get_raw_seqname
get_seqname
get_raw_start
get_start
get_raw_end
get_end
get_raw_name
get_name
get_raw_score
get_score
get_raw_strand
get_strand
get_raw_thickStart
get_thickStart
get_raw_thickEnd
get_thickEnd
get_raw_itemRgb
get_itemRgb
get_raw_blockCount
get_blockCount
get_raw_blockSizes
get_blockSizes
get_raw_blockStarts
get_blockStarts

PSL parser (Anne)

get_raw_Matches
get_matches
get_raw_misMatches
get_misMatches
get_raw_repMatches
get_repMatches
get_raw_nCount
get_nCount
get_raw_qNumInsert
get_qNumInsert
get_raw_qBaseInsert
get_qBaseInsert
get_raw_tNumInsert
get_tNumInsert
get_raw_tBaseInsert
get_tBaseInsert
get_raw_strand
get_strand
get_raw_qName
get_qName
get_raw_qSize
get_qSize
get_raw_qStart
get_qStart
get_raw_qEnd
get_qEnd
get_raw_tName
get_tName
get_raw_tSize
get_tSize
get_raw_tStart
get_tStart
get_raw_tEnd
get_tEnd
get_raw_blockCount
get_blockCount
get_raw_blockSizes
get_blockSizes
get_raw_qStarts
get_qStarts
get_raw_tStarts
get_tStarts

WIG parser (Anne)

Metadata:

get_feature_count
get_wiggle_type

Fields:

get_raw_chrom
get_seqname
get_raw_start
get_start
get_raw_end
get_end
get_raw_score
get_score

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GVF parser (Laurent):

get_metadata_key_list
get_gvf_version
get_genome_build
get_sequence_region_list
get_metadata_by_pragma
get_raw_seqname
get_seqname
get_raw_source
get_source
get_raw_type
get_type
get_raw_start
get_start
get_raw_end
get_end
get_raw_score
get_score
get_raw_strand
get_strand
get_raw_phase
get_phase
get_raw_attributes
get_attributes
get_ID
get_variant_seq
get_reference_seq

VCF parser (Laurent):

get_metadata_key_list
get_metadata_by_pragma
get_vcf_version
get_raw_seqname
get_seqname
get_raw_start
get_start
get_raw_end
get_end
get_outer_start
get_inner_start
get_inner_end
get_outer_end
get_raw_IDs
get_IDs
get_raw_reference
get_reference
get_raw_alternatives
get_alternatives
get_alternative_description
get_raw_score
get_score
get_raw_filter_results
get_filter_results
get_raw_info
get_info
get_info_description
get_raw_formats
get_formats
get_format_description
get_metadata_description
get_raw_individuals_info
get_individuals_info
get_individuals_genotypes

---------------------------------

EMF parser (Miguel)

get_sequences
get_score_types
tree
format
date
get_next_column

---------------------------------

BigBed Parser (Daniel)

get_chrom
get_start
get_end
get_score
get_parts
get_name
get_rgb
get_bedFeature

BigWig Parser (Daniel)

get_chrom
get_start
get_end
get_score