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[BDG-FORMATS-54] Generalizing the Fragment type #56

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48 changes: 29 additions & 19 deletions src/main/resources/avro/bdg.avdl
Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@ record Contig {
}

record AlignmentRecord {

/**
Read number within the array of fragment reads.
*/
Expand Down Expand Up @@ -259,34 +259,44 @@ record AlignmentRecord {
union { null, long } inferredInsertSize = null;
}

enum SequencingPlatform {
Illumina
}

record IlluminaInfo {
union { null, string } flowcellId;
union { null, int } lane;
union { null, int } tile;
union { null, int } surface;
union { null, int } xPosition;
union { null, int } yPosition;
}

record Sequence {
/**
Analogous to fastq
*/
union { null, string } sequenceName = null;
union { null, string } bases = null;
union { null, string } qualities = null;
union { null, SequencingPlatform } platformType = null;
union { null, IlluminaInfo } platformInfo = null;
}

/**
The DNA fragment that is was targeted by the sequencer, resulting in
one or more reads.
A set of reads that should be analyzed/stored together physically.
Typically the result of a groupby operation.
*/
record Fragment {
record Bucket {
/**
The name of this Fragment.
The name of this Bucket. Can include the group key in the logical
group-by operation.
*/
union { null, string } readName = null;

union { null, string } instrument = null;
union { null, string } runId = null;
union { null, string } bucketName = null;

/**
Fragment's insert size derived from alignment, if the reads have been
aligned.
The array of grouped reads. They may be unmapped.
*/
union { null, int } fragmentSize = null;

/**
The sequences read from this fragment.
*/
array<Sequence> sequences = [];
array<AlignmentRecord> alignments = [];
}

Expand Down Expand Up @@ -512,7 +522,7 @@ record VariantCallingAnnotations {
* 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.
Expand All @@ -523,7 +533,7 @@ record VariantCallingAnnotations {
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.
*/
Expand Down