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/**
* Licensed to Big Data Genomics (BDG) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The BDG licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
@namespace("org.bdgenomics.formats.avro")
protocol BDG {
/**
Record for describing a reference assembly. Not used for storing the contents
of said assembly.
*/
record Contig {
/**
The name of this contig in the assembly (e.g., "1").
*/
union { null, string } contigName = null;
/**
The length of this contig.
*/
union { null, long } contigLength = null;
/**
The MD5 checksum of the assembly for this contig.
*/
union { null, string } contigMD5 = null;
/**
The URL at which this reference assembly can be found.
*/
union { null, string } referenceURL = null;
/**
The name of this assembly (e.g., "hg19").
*/
union { null, string } assembly = null;
/**
The species that this assembly is for.
*/
union { null, string } species = null;
/**
Optional 0-based index of this contig in a SAM file header that it was read
from; helps output SAMs/BAMs with headers in the same order as they started
with, before a conversion to ADAM.
*/
union { null, int } referenceIndex = null;
}
/**
Description of a computational processing step.
*/
record ProcessingStep {
/**
The ID of this processing step.
*/
union { null, string } id = null;
/**
The name of the program used to run this step.
*/
union { null, string } programName = null;
/**
The command line used to run this step.
*/
union { null, string } commandLine = null;
/**
Previous processing step ID. Omit if this is the first step.
*/
union { null, string } previousId = null;
/**
The description of this processing step.
*/
union { null, string } description = null;
/**
The version of the tool that was run.
*/
union { null, string } version = null;
}
/**
Record group metadata.
*/
record RecordGroup {
/**
Record group identifier.
*/
union { null, string } name = null;
/**
Name of the sample that the record group is from.
*/
union { null, string } sample = null;
union { null, string } sequencingCenter = null;
union { null, string } description = null;
union { null, long } runDateEpoch = null;
union { null, string } flowOrder = null;
union { null, string } keySequence = null;
union { null, string } library = null;
union { null, int } predictedMedianInsertSize = null;
union { null, string } platform = null;
union { null, string } platformUnit = null;
/**
The processing steps that have been applied to this record group.
*/
array processingSteps = [];
}
/**
Alignment record.
*/
record AlignmentRecord {
/**
Read number within the array of fragment reads.
*/
union { int, null } readInFragment = 0;
/**
The reference sequence details for the reference chromosome that
this read is aligned to. If the read is unaligned, this field should
be null.
*/
union { null, string } contigName = null;
/**
0 based reference position for the start of this read's alignment.
Should be null if the read is unaligned.
*/
union { null, long } start = null;
/**
0 based reference position where this read used to start before
local realignment. Stores the same data as the OP field in the SAM format.
*/
union { null, long } oldPosition = null;
/**
0 based reference position for the end of this read's alignment.
Should be null if the read is unaligned.
*/
union { null, long } end = null;
/**
The global mapping quality of this read.
*/
union { null, int } mapq = null;
/**
The name of this read. This should be unique within the read group
that this read is from, and can be used to identify other reads that
are derived from a single fragment.
*/
union { null, string } readName = null;
/**
The bases in this alignment. If the read has been hard clipped, this may
not represent all the bases in the original read.
*/
union { null, string } sequence = null;
/**
The per-base quality scores in this alignment. If the read has been hard
clipped, this may not represent all the bases in the original read.
Additionally, if the error scores have been recalibrated, this field
will not contain the original base quality scores.
*/
union { null, string } qual = null;
/**
The Compact Ideosyncratic Gapped Alignment Report (CIGAR) string that
describes the local alignment of this read. Contains {length, operator}
pairs for all contiguous alignment operations. The operators include:
* M, ALIGNMENT_MATCH: An alignment match indicates that a sequence can be
aligned to the reference without evidence of an INDEL. Unlike the
SEQUENCE_MATCH and SEQUENCE_MISMATCH operators, the ALIGNMENT_MATCH
operator does not indicate whether the reference and read sequences are an
exact match.
* I, INSERT: The insert operator indicates that the read contains evidence of
bases being inserted into the reference.
* D, DELETE: The delete operator indicates that the read contains evidence of
bases being deleted from the reference.
* N, SKIP: The skip operator indicates that this read skips a long segment of
the reference, but the bases have not been deleted. This operator is
commonly used when working with RNA-seq data, where reads may skip long
segments of the reference between exons.
* S, CLIP_SOFT: The soft clip operator indicates that bases at the start/end
of a read have not been considered during alignment. This may occur if the
majority of a read maps, except for low quality bases at the start/end of
a read. Bases that are soft clipped will still be stored in the read.
* H, CLIP_HARD: The hard clip operator indicates that bases at the start/end of
a read have been omitted from this alignment. This may occur if this linear
alignment is part of a chimeric alignment, or if the read has been trimmed
(e.g., during error correction, or to trim poly-A tails for RNA-seq).
* P, PAD: The pad operator indicates that there is padding in an alignment.
* =, SEQUENCE_MATCH: This operator indicates that this portion of the aligned
sequence exactly matches the reference (e.g., all bases are equal to the
reference bases).
* X, SEQUENCE_MISMATCH: This operator indicates that this portion of the
aligned sequence is an alignment match to the reference, but a sequence
mismatch (e.g., the bases are not equal to the reference). This can
indicate a SNP or a read error.
*/
union { null, string } cigar = null;
/**
Stores the CIGAR string present before local indel realignment.
Stores the same data as the OC field in the SAM format.
*/
union { null, string } oldCigar = null;
/**
The number of bases in this read/alignment that have been trimmed from the
start of the read. By default, this is equal to 0. If the value is non-zero,
that means that the start of the read has been hard-clipped.
*/
union { int, null } basesTrimmedFromStart = 0;
/**
The number of bases in this read/alignment that have been trimmed from the
end of the read. By default, this is equal to 0. If the value is non-zero,
that means that the end of the read has been hard-clipped.
*/
union { int, null } basesTrimmedFromEnd = 0;
// Read flags (all default to false)
union { boolean, null } readPaired = false;
union { boolean, null } properPair = false;
union { boolean, null } readMapped = false;
union { boolean, null } mateMapped = false;
union { boolean, null } failedVendorQualityChecks = false;
union { boolean, null } duplicateRead = false;
/**
True if this alignment is mapped as a reverse compliment. This field
defaults to false.
*/
union { boolean, null } readNegativeStrand = false;
/**
True if the mate pair of this alignment is mapped as a reverse compliment.
This field defaults to false.
*/
union { boolean, null } mateNegativeStrand = false;
/**
This field is true if this alignment is either the best linear alignment,
or the first linear alignment in a chimeric alignment. Defaults to false.
*/
union { boolean, null } primaryAlignment = false;
/**
This field is true if this alignment is a lower quality linear alignment
for a multiply-mapped read. Defaults to false.
*/
union { boolean, null } secondaryAlignment = false;
/**
This field is true if this alignment is a non-primary linear alignment in
a chimeric alignment. Defaults to false.
*/
union { boolean, null } supplementaryAlignment = false;
// Commonly used optional attributes
union { null, string } mismatchingPositions = null;
union { null, string } origQual = null;
// Remaining optional attributes flattened into a string
union { null, string } attributes = null;
// record group identifer from sequencing run
union { null, string } recordGroupName = null;
union { null, string } recordGroupSample = null;
/**
The start position of the mate of this read. Should be set to null if the
mate is unaligned, or if the mate does not exist.
*/
union { null, long } mateAlignmentStart = null;
/**
The reference contig of the mate of this read. Should be set to null if the
mate is unaligned, or if the mate does not exist.
*/
union { null, string } mateContigName = null;
/**
The distance between this read and it's mate as inferred from alignment.
*/
union { null, long } inferredInsertSize = null;
}
/**
The DNA fragment that is was targeted by the sequencer, resulting in
one or more reads.
*/
record Fragment {
/**
The name of this fragment.
*/
union { null, string } readName = null;
union { null, string } instrument = null;
union { null, string } runId = null;
/**
Fragment's insert size derived from alignment, if the reads have been
aligned.
*/
union { null, int } fragmentSize = null;
/**
The sequences read from this fragment.
*/
array alignments = [];
}
/**
Stores a contig of nucleotides; this may be a reference chromosome, may be an
assembly, may be a BAC. Very long contigs (>1Mbp) need to be split into fragments.
It seems that they are too long to load in a single go. For best performance,
it seems like 10kbp is a good point at which to start splitting contigs into
fragments.
*/
record NucleotideContigFragment {
/**
The name of this contig in the assembly (e.g., "1").
*/
union { null, string } contigName = null;
/**
The total length of the contig this fragment is from.
*/
union { null, long } contigLength = null;
/**
A description for this contig. When importing from FASTA, the FASTA header
description line should be stored here.
*/
union { null, string } description = null;
/**
The sequence of bases in this fragment.
*/
union { null, string } sequence = null;
/**
In a fragmented contig, the index of this fragment in the set of fragments.
Can be null if the contig is not fragmented.
*/
union { null, int } index = null;
/**
The position of the first base of this fragment in the overall contig. E.g.,
if all fragments are 10kbp and this is the third fragment in the contig,
the start position would be 20000L.
*/
union { null, long } start = null;
/**
The position of the last base of this fragment in the overall contig. E.g.,
if all fragments are 10kbp and this is the third fragment in the contig,
the end position would be 29999L.
*/
union { null, long } end = null;
/**
The length of this fragment.
*/
union { null, long } length = null;
/**
The total count of fragments that this contig has been broken into. Can be
null if the contig is not fragmented.
*/
union { null, int } fragments = null;
}
/**
Errors, warnings, or informative messages regarding variant annotation accuracy.
*/
enum VariantAnnotationMessage {
/**
Chromosome does not exist in reference genome database. Typically indicates
a mismatch between the chromosome names in the input file and the chromosome
names used in the reference genome. Message code E1.
*/
ERROR_CHROMOSOME_NOT_FOUND,
/**
The variant's genomic coordinate is greater than chromosome's length.
Message code E2.
*/
ERROR_OUT_OF_CHROMOSOME_RANGE,
/**
The 'REF' field in the input VCF file does not match the reference genome.
This warning may indicate a conflict between input data and data from
reference genome (for instance is the input VCF was aligned to a different
reference genome). Message code W1.
*/
WARNING_REF_DOES_NOT_MATCH_GENOME,
/**
Reference sequence is not available, thus no inference could be performed.
Message code W2.
*/
WARNING_SEQUENCE_NOT_AVAILABLE,
/**
A protein coding transcript having a nonmultiple of 3 length. It indicates
that the reference genome has missing information about this particular
transcript. Message code W3.
*/
WARNING_TRANSCRIPT_INCOMPLETE,
/**
A protein coding transcript has two or more STOP codons in the middle of
the coding sequence (CDS). This should not happen and it usually means the
reference genome may have an error in this transcript. Message code W4.
*/
WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS,
/**
A protein coding transcript does not have a proper START codon. It is
rare that a real transcript does not have a START codon, so this probably
indicates an error or missing information in the reference genome.
Message code W5.
*/
WARNING_TRANSCRIPT_NO_START_CODON,
/**
Variant has been realigned to the most 3prime position within the
transcript. This is usually done to to comply with HGVS specification
to always report the most 3prime annotation. Message code I1.
*/
INFO_REALIGN_3_PRIME,
/**
This effect is a result of combining more than one variants (e.g. two
consecutive SNPs that conform an MNP, or two consecutive frame_shift
variants that compensate frame). Message code I2.
*/
INFO_COMPOUND_ANNOTATION,
/**
An alternative reference sequence was used to calculate this annotation
(e.g. cancer sample comparing somatic vs. germline). Message code I3.
*/
INFO_NON_REFERENCE_ANNOTATION
}
/**
Annotation of a variant in the context of a feature, typically a transcript.
*/
record TranscriptEffect {
/**
Alternate allele for this variant annotation.
*/
union { null, string } alternateAllele = null;
/**
One or more annotations (also referred to as effects or consequences) of the
variant in the context of the feature identified by featureId. Must be
Sequence Ontology (SO, see http://www.sequenceontology.org) term names, e.g.
stop_gained, missense_variant, synonymous_variant, upstream_gene_variant.
*/
array effects = [];
/**
Common gene name (HGNC), e.g. BRCA2. May be closest gene if annotation
is intergenic.
*/
union { null, string } geneName = null;
/**
Gene identifier, e.g. Ensembl Gene identifier, ENSG00000139618. May be
closest gene if annotation is intergenic.
*/
union { null, string } geneId = null;
/**
Feature type, may use Sequence Ontology term names. Typically transcript.
*/
union { null, string } featureType = null;
/**
Feature identifier, e.g. Ensembl Transcript identifier and version, ENST00000380152.7.
*/
union { null, string } featureId = null;
/**
Feature biotype, e.g. Protein coding or Non coding. See http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html.
*/
union { null, string } biotype = null;
/**
Intron or exon rank.
*/
union { null, int } rank = null;
/**
Total number of introns or exons.
*/
union { null, int } total = null;
/**
HGVS.g description of the variant. See http://www.hgvs.org/mutnomen/recs-DNA.html.
*/
union { null, string } genomicHgvs = null;
/**
HGVS.c description of the variant. See http://www.hgvs.org/mutnomen/recs-DNA.html.
*/
union { null, string } transcriptHgvs = null;
/**
HGVS.p description of the variant, if coding. See http://www.hgvs.org/mutnomen/recs-prot.html.
*/
union { null, string } proteinHgvs = null;
/**
cDNA sequence position (one based).
*/
union { null, int } cdnaPosition = null;
/**
cDNA sequence length in base pairs (one based).
*/
union { null, int } cdnaLength = null;
/**
Coding sequence position (one based, includes START and STOP codons).
*/
union { null, int } cdsPosition = null;
/**
Coding sequence length in base pairs (one based, includes START and STOP codons).
*/
union { null, int } cdsLength = null;
/**
Protein sequence position (one based, includes START but not STOP).
*/
union { null, int } proteinPosition = null;
/**
Protein sequence length in amino acids (one based, includes START but not STOP).
*/
union { null, int } proteinLength = null;
/**
Distance in base pairs to the feature.
*/
union { null, int } distance = null;
/**
Zero or more errors, warnings, or informative messages regarding variant annotation accuracy.
*/
array messages = [];
}
/**
Variant annotation.
*/
record VariantAnnotation {
/**
Ancestral allele, VCF INFO reserved key AA, Number=1, shared across all alternate
alleles in the same VCF record.
*/
union { null, string } ancestralAllele = null;
/**
Allele count, VCF INFO reserved key AC, Number=A, split for multi-allelic sites into
a single integer value.
*/
union { null, int } alleleCount = null;
/**
Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic
sites into single integer values for the reference allele (referenceReadDepth) and
the alternate allele (readDepth, this field).
*/
union { null, int } readDepth = null;
/**
Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for
multi-allelic sites into single integer values for the reference allele
(referenceForwardReadDepth) and the alternate allele (forwardReadDepth, this field).
*/
union { null, int } forwardReadDepth = null;
/**
Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for
multi-allelic sites into single integer values for the reference allele
(referenceReverseReadDepth) and the alternate allele (reverseReadDepth, this field).
*/
union { null, int } reverseReadDepth = null;
/**
Total read depth, VCF INFO reserved key AD, Number=R, split for multi-allelic
sites into single integer values for the reference allele (referenceReadDepth, this field)
and the alternate allele (readDepth).
*/
union { null, int } referenceReadDepth = null;
/**
Forward strand read depth, VCF INFO reserved key ADF, Number=R, split for
multi-allelic sites into single integer values for the reference allele
(referenceForwardReadDepth, this field) and the alternate allele (forwardReadDepth).
*/
union { null, int } referenceForwardReadDepth = null;
/**
Reverse strand read depth, VCF INFO reserved key ADR, Number=R, split for
multi-allelic sites into single integer values for the reference allele
(referenceReverseReadDepth, this field) and the alternate allele (reverseReadDepth).
*/
union { null, int } referenceReverseReadDepth = null;
/**
Minor allele frequency, VCF INFO reserved key AF, Number=A, split for multi-allelic
sites into a single float value. Use this when frequencies are estimated from primary
data, not calculated from called genotypes.
*/
union { null, float } alleleFrequency = null;
/**
CIGAR string describing how to align an alternate allele to the reference
allele, VCF INFO reserved key CIGAR, Number=A, split for multi-allelic sites into
a single string value.
*/
union { null, string } cigar = null;
/**
Membership in dbSNP, VCF INFO reserved key DB, Number=0. Until Number=A and
Number=R flags are supported by the VCF specification, this value is shared
across all alternate alleles in the same VCF record.
*/
union { null, boolean } dbSnp = null;
/**
Membership in HapMap2, VCF INFO reserved key H2, Number=0. Until Number=A and
Number=R flags are supported by the VCF specification, this value is shared
across all alternate alleles in the same VCF record.
*/
union { null, boolean } hapMap2 = null;
/**
Membership in HapMap3, VCF INFO reserved key H3, Number=0. Until Number=A and
Number=R flags are supported by the VCF specification, this value is shared
across all alternate alleles in the same VCF record.
*/
union { null, boolean } hapMap3 = null;
/**
Validated by follow up experiment, VCF INFO reserved key VALIDATED, Number=0.
Until Number=A and Number=R flags are supported by the VCF specification, this
value is shared across all alternate alleles in the same VCF record.
*/
union { null, boolean } validated = null;
/**
Membership in 1000 Genomes, VCF INFO reserved key 1000G, Number=0. Until
Number=A and Number=R flags are supported by the VCF specification, this
value is shared across all alternate alleles in the same VCF record.
*/
union { null, boolean } thousandGenomes = null;
/**
True if this variant call is somatic; in this case, the reference allele will
have been observed in another sample. VCF INFO reserved key "SOMATIC", Number=0.
Until Number=A and Number=R flags are supported by the VCF specification, this value
is shared across all alleles in the same VCF record.
*/
union { boolean, null } somatic = false;
/**
Zero or more transcript effects, predicted by a tool such as SnpEff or Ensembl VEP,
one per transcript (or other feature). VCF INFO key ANN, split for multi-allelic
sites. See http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf.
*/
array transcriptEffects = [];
/**
Additional variant attributes that do not fit into the standard fields above.
The values are stored as strings, even for flag, integer, and float types. VCF
INFO key values with Number=., Number=0, Number=1, and Number=[n] are shared across
all alternate alleles in the same VCF record. VCF INFO key values with Number=A are
split for multi-allelic sites into a single value. VCF INFO key values with Number=R
are split into an array of two values, [reference allele, alternate allele], separated
by commas, e.g. "0,1".
*/
map attributes = {};
}
/**
Variant.
*/
record Variant {
/**
The reference contig this variant exists on. VCF column 1 "CONTIG".
*/
union { null, string } contigName = null;
/**
The zero-based start position of this variant on the reference contig.
VCF column 2 "POS" converted to zero-based coordinate system, closed-open intervals.
*/
union { null, long } start = null;
/**
The zero-based, exclusive end position of this variant on the reference contig.
Calculated by start + referenceAllele.length().
*/
union { null, long } end = null;
/**
Zero or more unique names or identifiers for this variant. If this is a dbSNP
variant it is encouraged to use the rs number(s). VCF column 3 "ID" shared across
all alleles in the same VCF record.
*/
array names = [];
/**
A string describing the reference allele at this site. VCF column 4 "REF".
*/
union { null, string } referenceAllele = null;
/**
A string describing the alternate allele at this site. VCF column 5 "ALT" split
for multi-allelic sites.
*/
union { null, string } alternateAllele = null;
/**
True if filters were applied for this variant. VCF column 7 "FILTER" any value other
than the missing value.
*/
union { null, boolean } filtersApplied = null;
/**
True if all filters for this variant passed. VCF column 7 "FILTER" value PASS.
*/
union { null, boolean } filtersPassed = null;
/**
Zero or more filters that failed for this variant. VCF column 7 "FILTER" shared across
all alleles in the same VCF record.
*/
array filtersFailed = [];
/**
Annotation for this variant, if any.
*/
union { null, VariantAnnotation } annotation = null;
}
/**
An enumeration that describes the allele that corresponds to a genotype.
*/
enum GenotypeAllele {
/**
The genotype is the reference allele.
*/
REF,
/**
The genotype is the alternate allele.
*/
ALT,
/**
The genotype is an unspecified other alternate allele. This occurs in our schema
when we have split a multi-allelic genotype into two genotype records.
*/
OTHER_ALT,
/**
The genotype could not be called.
*/
NO_CALL
}
/**
An enumeration that describes the characteristics of a genotype at a site.
*/
enum GenotypeType {
/**
All genotypes at this site were called as the reference allele.
*/
HOM_REF,
/**
Genotypes at this site were called as multiple different alleles. This
most commonly occurs if a diploid sample's genotype contains one reference
and one variant allele, but can also occur if the genotype contains multiple
alternate alleles.
*/
HET,
/**
All genotypes at this site were called as a single alternate allele.
*/
HOM_ALT,
/**
The genotype could not be called at this site.
*/
NO_CALL
}
/**
This record represents all stats that, inside a VCF, are stored outside of the
sample but are computed based on the samples. For instance, MAPQ0 is an aggregate
stat computed from all samples and stored inside the INFO line.
*/
record VariantCallingAnnotations {
/**
True if filters were applied for this genotype call. FORMAT field "FT" any value other
than the missing value.
*/
union { null, boolean } filtersApplied = null;
/**
True if all filters for this genotype call passed. FORMAT field "FT" value PASS.
*/
union { null, boolean } filtersPassed = null;
/**
Zero or more filters that failed for this genotype call from FORMAT field "FT".
*/
array filtersFailed = [];
/**
True if the reads covering this site were randomly downsampled to reduce coverage.
*/
union { null, boolean } downsampled = null;
/**
The Wilcoxon rank-sum test statistic of the base quality scores. The base quality
scores are separated by whether or not the base supports the reference or the
alternate allele.
*/
union { null, float } baseQRankSum = null;
/**
The Fisher's exact test score for the strand bias of the reference and alternate
alleles. Stored as a phred scaled probability. Thus, if:
* a = The number of positive strand reads covering the reference allele
* b = The number of positive strand reads covering the alternate allele
* c = The number of negative strand reads covering the reference allele
* d = The number of negative strand reads covering the alternate allele
This value takes the score:
-10 log((a + b)! * (c + d)! * (a + c)! * (b + d)! / (a! b! c! d! n!)
Where n = a + b + c + d.
*/
union { null, float } fisherStrandBiasPValue = null;
/**
The root mean square of the mapping qualities of reads covering this site.
*/
union { null, float } rmsMapQ = null;
/**
The number of reads at this site with mapping quality equal to 0.
*/
union { null, int } mapq0Reads = null;
/**
The Wilcoxon rank-sum test statistic of the mapping quality scores. The mapping
quality scores are separated by whether or not the read supported the reference or the
alternate allele.
*/
union { null, float } mqRankSum = null;
/**
The Wilcoxon rank-sum test statistic of the position of the base in the read at this site.
The positions are separated by whether or not the base supports the reference or the
alternate allele.
*/
union { null, float } readPositionRankSum = null;
/**
The log scale prior probabilities of the various genotype states at this site.
The number of elements in this array should be equal to the ploidy at this
site, plus 1.
*/
array genotypePriors = [];
/**
The log scaled posterior probabilities of the various genotype states at this site,
in this sample. The number of elements in this array should be equal to the ploidy at
this site, plus 1.
*/
array genotypePosteriors = [];
/**
The log-odds ratio of being a true vs. false variant under a trained statistical model.
This model can be a multivariate Gaussian mixture, support vector machine, etc.
*/
union { null, float } vqslod = null;
/**
If known, the feature that contributed the most to this variant being classified as
a false variant.
*/
union { null, string } culprit = null;
/**
Additional feature info that doesn't fit into the standard fields above.
They are all encoded as (string, string) key-value pairs.
*/
map attributes = {};
}
/**
Genotype.
*/
record Genotype {
/**
The variant called at this site.
*/
union { null, Variant } variant = null;
/**
The reference contig that this genotype's variant exists on.
*/
union { null, string } contigName = null;
/**
The 0-based start position of this genotype's variant on the reference contig.
*/
union { null, long } start = null;
/**
The 0-based, exclusive end position of this genotype's variant on the reference contig.
*/
union { null, long } end = null;
/**
Statistics collected at this site, if available.
*/
union { null, VariantCallingAnnotations } variantCallingAnnotations = null;
/**
The unique identifier for this sample.
*/
union { null, string } sampleId = null;
/**
A description of this sample.
*/
union { null, string } sampleDescription = null;
/**
A string describing the provenance of this sample and the processing applied
in genotyping this sample.
*/
union { null, string } processingDescription = null;
/**
An array describing the genotype called at this site. The length of this
array is equal to the ploidy of the sample at this site. This array may
reference OTHER_ALT alleles if this site is multi-allelic in this sample.
*/
array alleles = [];
/**
The expected dosage of the alternate allele in this sample.
*/
union { null, float } expectedAlleleDosage = null;
/**
The number of reads that show evidence for the reference at this site.
*/
union { null, int } referenceReadDepth = null;
/**
The number of reads that show evidence for this alternate allele at this site.
*/
union { null, int } alternateReadDepth = null;
/**
The total number of reads at this site. May not equal (alternateReadDepth +
referenceReadDepth) if this site shows evidence of multiple alternate alleles.
Analogous to VCF's DP.
*/
union { null, int } readDepth = null;
/**
The minimum number of reads seen at this site across samples when joint
calling variants. Analogous to VCF's MIN_DP.
*/
union { null, int } minReadDepth = null;
/**
The phred-scaled probability that we're correct for this genotype call.
Analogous to VCF's GQ.
*/
union { null, int } genotypeQuality = null;
/**
Log scaled likelihoods that we have n copies of this alternate allele.
The number of elements in this array should be equal to the ploidy at this
site, plus 1. Analogous to VCF's PL.
*/
array genotypeLikelihoods = [];
/**
Log scaled likelihoods that we have n non-reference alleles at this site.
The number of elements in this array should be equal to the ploidy at this
site, plus 1.
*/
array nonReferenceLikelihoods = [];
/**
Component statistics which comprise the Fisher's Exact Test to detect strand bias.
If populated, this element should have length 4.
*/
array strandBiasComponents = [];
/**
We split multi-allelic VCF lines into multiple single-alternate records.
This bit is set if that happened for this record.
*/
union { boolean, null } splitFromMultiAllelic = false;
/**
True if this genotype is phased.
*/
union { boolean, null } phased = false;
/**
The ID of this phase set, if this genotype is phased. Should only be populated
if phased == true; else should be null.
*/
union { null, int } phaseSetId = null;
/**
Phred scaled quality score for the phasing of this genotype, if this genotype
is phased. Should only be populated if phased == true; else should be null.
*/
union { null, int } phaseQuality = null;
}
/**
Strand of an alignment or feature.
*/
enum Strand {
/**
Forward ("+") strand.
*/
FORWARD,
/**
Reverse ("-") strand.
*/
REVERSE,
/**
Independent or not stranded (".").
*/
INDEPENDENT,
/**
Strandedness is relevant, but unknown ("?").
*/
UNKNOWN
}
/**
Database cross reference in GFF3 style DBTAG:ID format.
*/
record Dbxref {
/**
Database tag in GFF3 style DBTAG:ID format, e.g. EMBL in EMBL:AA816246.
*/
union { null, string } db = null;
/**
Accession number in GFF3 style DBTAG:ID format, e.g. AA816246 in EMBL:AA816246.
*/
union { null, string } accession = null;
}
/**
Ontology term cross reference in GFF3 style DBTAG:ID format.
*/
record OntologyTerm {
/**
Ontology abbreviation in GFF3 style DBTAG:ID format, e.g. GO in GO:0046703.
*/
union { null, string } db = null;
/**
Ontology term accession number or identifer in GFF3 style DBTAG:ID format,
e.g. 0046703 in GO:0046703.
*/
union { null, string } accession = null;
}
/**
Feature, such as those represented in native file formats BED, GFF2/GTF,
GFF3, IntervalList, and NarrowPeak.
*/
record Feature {
/**
Identifier for this feature. ID tag in GFF3.
*/
union { null, string } featureId = null;
/**
Display name for this feature, e.g. DVL1. Name tag in GFF3, optional column 4 "name"
in BED format.
*/
union { null, string } name = null;
/**
Source of this feature, typically the algorithm or operating procedure that generated
this feature, e.g. GeneWise. Column 2 "source" in GFF3.
*/
union { null, string } source = null;
/**
Feature type, constrained by some formats to a term from the Sequence Ontology (SO),
e.g. gene, mRNA, exon, or a SO accession number (SO:0000704, SO:0000234, SO:0000147,
respectively). Column 3 "type" in GFF3.
*/
union { null, string } featureType = null;
/**
Contig this feature is located on. Column 1 "seqid" in GFF3, column 1 "chrom"
in BED format.
*/
union { null, string } contigName = null;
/**
Start position for this feature, in 0-based coordinate system with closed-open
intervals. This may require conversion from the coordinate system of the native
file format. Column 4 "start" in GFF3, column 2 "chromStart" in BED format.
*/
union { null, long } start = null;
/**
End position for this feature, in 0-based coordinate system with closed-open
intervals. This may require conversion from the coordinate system of the native
file format. Column 5 "end" in GFF3, column 3 "chromEnd" in BED format.
*/
union { null, long } end = null;
/**
Strand for this feature. Column 7 "strand" in GFF3, optional column 6 "strand"
in BED format.
*/
union { null, Strand } strand = null;
/**
For features of type "CDS", the phase indicates where the feature begins with reference
to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number
of bases that should be removed from the beginning of this feature to reach the first base
of the next codon. Column 8 "phase" in GFF3.
*/
union { null, int } phase = null;
/**
For features of type "CDS", the frame indicates whether the first base of the CDS segment is
the first (frame 0), second (frame 1) or third (frame 2) in the codon of the ORF. Column 8
"frame" in GFF2/GTF format.
*/
union { null, int } frame = null;
/**
Score for this feature. Column 6 "score" in GFF3, optional column 5
"score" in BED format.
*/
union { null, double } score = null;
/**
Gene identifier, e.g. ENSG00000107404. gene_id tag in GFF2/GTF.
*/
union { null, string } geneId = null;
/**
Transcript identifier, e.g. ENST00000378891. transcript_id tag in GFF2/GTF.
*/
union { null, string } transcriptId = null;
/**
Exon identifier, e.g. ENSE00001479184. exon_id tag in GFF2/GTF.
*/
union { null, string } exonId = null;
/**
Secondary names or identifiers for this feature. Alias tag in GFF3.
*/
array aliases = [];
/**
Parent feature identifiers. Parent tag in GFF3.
*/
array parentIds = [];
/**
Target of a nucleotide-to-nucleotide or protein-to-nucleotide alignment
feature. The format of the value is "target_id start end [strand]", where
strand is optional and may be "+" or "-". Target tag in GFF3.
*/
union { null, string } target = null;
/**
Alignment of the feature to the target in CIGAR format. Gap tag in GFF3.
*/
union { null, string } gap = null;
/**
Used to disambiguate the relationship between one feature and another when
the relationship is a temporal one rather than a purely structural "part of"
one. Derives_from tag in GFF3.
*/
union { null, string } derivesFrom = null;
/**
Notes or comments for this feature. Note tag in GFF3.
*/
array notes = [];
/**
Database cross references for this feature. Dbxref tag in GFF3.
*/
array dbxrefs = [];
/**
Ontology term cross references for this feature. Ontology_term tag in GFF3.
*/
array ontologyTerms = [];
/**
True if this feature is circular. Is_circular tag in GFF3.
*/
union { null, boolean } circular = null;
/**
Additional feature attributes. Column 9 "attributes" in GFF3, excepting those
reserved tags parsed into other fields, such as parentIds, dbxrefs, and ontologyTerms.
*/
map attributes = {};
}
/**
Sample.
*/
record Sample {
/**
Identifier for this sample, e.g. IDENTIFIERS → PRIMARY_ID or other
subelements of IDENTIFERS in SRA metadata, sample tag SM in read group @RG header lines
in SAM/BAM files, or sample ID from the header or ##SAMPLE=<ID=S_ID meta-information
lines in VCF files.
*/
union { null, string } sampleId = null;
/**
Descriptive name for this sample, e.g. SAMPLE_NAME → TAXON_ID, COMMON_NAME,
INDIVIDUAL_NAME, or other subelements of SAMPLE_NAME in SRA metadata.
*/
union { null, string } name = null;
/**
Map of attributes. Common attributes may include: SRA metadata not mentioned above,
e.g. SAMPLE → TITLE, SAMPLE → DESCRIPTION, and SAMPLE_ATTRIBUTES; ENA default
sample checklist attributes such as cell_type, dev_stage, and germline; and Genomes,
Mixture, and Description from sample meta-information lines in VCF files.
*/
map attributes = {};
/**
The processing steps that have been applied to this sample.
*/
array processingSteps = [];
}
/**
Alphabet.
*/
enum Alphabet {
/**
DNA alphabet.
*/
DNA,
/**
RNA alphabet.
*/
RNA,
/**
Protein alphabet.
*/
PROTEIN
}
/**
Contiguous sequence from an alphabet, e.g. a DNA contig, an RNA transcript,
or a protein translation.
*/
record Sequence {
/**
Name of this sequence.
*/
union { null, string } name = null;
/**
Description for this sequence.
*/
union { null, string } description = null;
/**
Alphabet for this sequence, defaults to Alphabet.DNA.
*/
union { Alphabet, null } alphabet = "DNA";
/**
Sequence.
*/
union { null, string } sequence = null;
/**
Length of this sequence.
*/
union { null, long } length = null;
/**
Map of attributes.
*/
map attributes = {};
}
/**
View of a contiguous region of a sequence.
*/
record Slice { // extends Sequence
/**
Name of the sequence this slice views.
*/
union { null, string } name = null;
/**
Description for the sequence this slice views.
*/
union { null, string } description = null;
/**
Alphabet for the sequence this slice views, defaults to Alphabet.DNA.
*/
union { Alphabet, null } alphabet = "DNA";
/**
Sequence for this slice.
*/
union { null, string } sequence = null;
/**
Start position for this slice on the sequence this slice views, in 0-based coordinate
system with closed-open intervals.
*/
union { null, long } start = null;
/**
End position for this slice on the sequence this slice views, in 0-based coordinate
system with closed-open intervals.
*/
union { null, long } end = null;
/**
Strand for this slice, if any, defaults to Strand.INDEPENDENT.
*/
union { Strand, null } strand = "INDEPENDENT";
/**
Length of this slice.
*/
union { null, long } length = null;
/**
Length of the sequence this slice views.
*/
union { null, long } totalLength = null;
/**
Index of this slice in a set of slices that covers the sequence this slice views, if any.
*/
union { null, int } index = null;
/**
Number of slices in a set of slices that covers the sequence this slice views, if any.
*/
union { null, int } slices = null;
/**
Map of attributes.
*/
map attributes = {};
}
/**
Quality score variant.
*/
enum QualityScoreVariant {
/**
Sanger and Illumina version >= 1.8 FASTQ quality score variant.
*/
FASTQ_SANGER,
/**
Solexa and Illumina version 1.0 FASTQ quality score variant.
*/
FASTQ_SOLEXA,
/**
Illumina version >= 1.3 and < 1.8 FASTQ quality score variant.
*/
FASTQ_ILLUMINA
}
/**
Sequence with quality scores.
*/
record Read { // extends Sequence
/**
Name of this read.
*/
union { null, string } name = null;
/**
Description for this read.
*/
union { null, string } description = null;
/**
Alphabet for this read, defaults to Alphabet.DNA.
*/
union { Alphabet, null } alphabet = "DNA";
/**
Sequence for this read.
*/
union { null, string } sequence = null;
/**
Length of this read.
*/
union { null, long } length = null;
/**
Quality scores for this read.
*/
union { null, string } qualityScores = null;
/**
Quality score variant for this read, defaults to QualityScoreVariant.FASTQ_SANGER.
*/
union { QualityScoreVariant, null } qualityScoreVariant = "FASTQ_SANGER";
/**
Map of attributes.
*/
map attributes = {};
}
}
