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syntax = "proto2";
package org.campagnelab.dl.varanalysis.protobuf;
option java_package = "org.campagnelab.dl.varanalysis.protobuf";
option optimize_for = SPEED;
/**
One such message per position in the genome that we observe. These records will be written to collections and
packed in a binary file.
*/
message BaseInformationCollection {
repeated BaseInformation records = 1;
}
message BaseInformation {
/** Index of the reference sequence where this base is observed in the genome. */
required uint32 reference_index = 1;
/** Identifier for the reference sequence (typically chromosome name). */
optional string reference_id = 10;
/** The position in the reference sequence of the genome. */
required uint32 position = 2;
/** Whether this base was mutated in simulation. */
optional bool mutated = 3;
/** The base we have introduced in the simulation. Always length 1. */
optional string mutatedBase = 4;
/** The index of the counts array where the mutated element was introduced. */
optional uint32 indexOfMutatedBase = 7;
/** The frequency with which this base was mutated by the mutator. */
optional float frequencyOfMutation = 6;
/**
The base present at the position in the genome/reference sequence.
*/
optional string referenceBase = 5;
/** A set of samples (ie germline,somatic). */
repeated SampleInfo samples = 8;
/** The genotype at this base position. In the format A/B where A,B are alleles (single bases or indels).
Homozygotes are written for instance, A/A while A/T-- is a heterozygote genotype with one allele A another T--*[ */
optional string trueGenotype = 9;
/** This should generally correspond with the reference base, but in the case of some indels will be different.
Eg: A (snp or no variant) , A--- (insertion) or ACAG. (deletion)[ */
optional string trueFrom = 11;
/** Genomic context centered on the base: bases around the base. If 11 bases are stored, 5 bases of context are
stored on either side. */
optional string genomicSequenceContext = 15;
/** gobyGenotypeIndex corresponding to each called allele of the true genotype **/
repeated uint32 calledCountIndices = 16;
}
/**
Usually two SampleInfo messages, one germline and one somatic. Contain data about the samples the count info for each genotype.
*/
message SampleInfo {
/** A number of bases were observed at the position. */
repeated CountInfo counts = 1;
/** Flag to specify whether the relevant sample is from a tumor (ie somatic sample) */
optional bool isTumor = 2;
/** String encoding nicely formatted version of counts */
optional string formattedCounts = 3;
/** Indicates whether this sample has a non-reference allele. Only filled in
when true labels have been added (using add-true-genotypes.sh from variationanalysis).
*/
optional bool isVariant = 4;
/** The genotype at this base position, in this sample. In the format A/B where A,B are alleles (single bases or indels).
Homozygotes are written for instance, A/A while A/T-- is a heterozygote genotype with one allele A another T--*[
*/
optional string trueGenotype = 5;
/** The genotype before segment post-processing. Used for debugging post-processing of segment construction. **/
optional string prePostProcessingGenotype=100;
/** gobyGenotypeIndex corresponding to each called allele of the true genotype **/
repeated uint32 calledCountIndices = 9;
}
message CountInfo {
/**
True iff genotype sequence observed in the sample matches the reference sequence. */
required bool matchesReference = 1;
/**
Sequence of the genotype observed in the reference genome. Typically a single base, or an indel sequence. */
required string fromSequence = 2;
/**
Sequence of the genotype observed in the sample. Typically a single base, or an indel sequence. */
required string toSequence = 3;
/** The number of times the genotype is observed in the sample in a read matching the forward strand. */
required uint32 genotypeCountForwardStrand = 4;
/** The number of times the genotype is observed in the sample in a read matching the reverse strand. */
required uint32 genotypeCountReverseStrand = 5;
/**
Indicates whether this genotype is an indel. */
optional bool isIndel = 15;
/** The quality scores of all bases matching this genotype on the forward strand. Phred scale. */
repeated NumberWithFrequency qualityScoresForwardStrand = 16;
/** The quality scores of all bases matching this genotype on the reverse strand. Phred scale. */
repeated NumberWithFrequency qualityScoresReverseStrand = 17;
/** The index in the read of all bases matching this genotype on the forward strand */
repeated NumberWithFrequency readIndicesForwardStrand = 18;
/** The index in the read of all bases matching this genotype on the reverse strand */
repeated NumberWithFrequency readIndicesReverseStrand = 19;
/** Mapping qualities for read on the forward strand with this genotype. */
repeated NumberWithFrequency readMappingQualityForwardStrand = 21;
/** Mapping qualities for read on the reverse strand with this genotype. */
repeated NumberWithFrequency readMappingQualityReverseStrand = 22;
/**
Number of variations found in the reads that support this genotype. */
repeated NumberWithFrequency numVariationsInReads = 23;
/**
Insert sizes found in reads that support this genotype. */
repeated NumberWithFrequency insertSizes = 24;
/**
Target aligned lengths for aligned reads that support this genotype. */
repeated NumberWithFrequency targetAlignedLengths = 25;
/**
Query aligned lengths for aligned reads that support this genotype. **/
repeated NumberWithFrequency queryAlignedLengths = 26;
/**
Query positions for aligned reads that support this genotype. **/
repeated NumberWithFrequency queryPositions = 30;
/**
Pair flags for aligned reads that support this genotype. **/
repeated NumberWithFrequency pairFlags = 27;
/** The index in the read of all bases matching this genotype on the forward strand */
repeated NumberWithFrequency distancesToReadVariationsForwardStrand = 28;
/** The index in the read of all bases matching this genotype on the reverse strand */
repeated NumberWithFrequency distancesToReadVariationsReverseStrand = 29;
/** Number of bases between the base where the variation is observed and the start of the read. */
repeated NumberWithFrequency distanceToStartOfRead = 31;
/** Number of bases between the base where the variation is observed and the end of the read. */
repeated NumberWithFrequency distanceToEndOfRead = 32;
/** True iff the genotype is called in this sample. In other words, this field is true when the genotype caller believes
that this genotype is present in the sample. */
optional bool isCalled = 20;
/*
The index of the genotype in the sample count info array. Used when counts are sorted and we need to restore
the original genotype order.
*/
optional uint32 gobyGenotypeIndex = 40;
/** The offset used when creating the record copy during post-processing. Used for debugging post-processing of segment construction. */
optional uint32 offset=101;
}
message NumberWithFrequency {
required int32 number = 1;
required uint32 frequency = 2;
}
message SomaticOutput {
required bool isSomatic = 200;
/** Index of the reference sequence where this base is observed in the genome. */
required uint32 reference_index = 1;
/** Identifier for the reference sequence (typically chromosome name). */
optional string reference_id = 10;
/** The position in the reference sequence of the genome. */
required uint32 position = 2;
/** The base we have introduced in the simulation. Always length 1. */
optional string mutatedBase = 4;
/** The index of the counts array where the mutated element was introduced. */
optional uint32 indexOfMutatedBase = 7;
/** The frequency with which this base was mutated by the mutator. */
optional float frequencyOfMutation = 6;
/**
The base present at the position in the genome/reference sequence.
*/
optional string referenceBase = 5;
}
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