diff --git a/src/main/resources/avro/common.avdl b/src/main/resources/avro/common.avdl index 911a8e4d..8aebe74c 100644 --- a/src/main/resources/avro/common.avdl +++ b/src/main/resources/avro/common.avdl @@ -33,6 +33,7 @@ record GAPosition { /** The 0-based offset from the start of the forward strand for that reference. + Genomic positions are non-negative integers less than reference length. */ long position; diff --git a/src/main/resources/avro/readmethods.avdl b/src/main/resources/avro/readmethods.avdl index edf64a95..5216b814 100644 --- a/src/main/resources/avro/readmethods.avdl +++ b/src/main/resources/avro/readmethods.avdl @@ -33,6 +33,9 @@ record GASearchReadsRequest { /** The start position (0-based) of this query. If a reference is specified, this defaults to 0. + Genomic positions are non-negative integers less than reference length. + Requests spanning the join of circular genomes are represented as + two requests one on each side of the join (position 0). */ union { null, long } start = 0; diff --git a/src/main/resources/avro/referencemethods.avdl b/src/main/resources/avro/referencemethods.avdl index 48887096..33c4c446 100644 --- a/src/main/resources/avro/referencemethods.avdl +++ b/src/main/resources/avro/referencemethods.avdl @@ -171,6 +171,9 @@ example: record GAListReferenceBasesRequest { /** The start position (0-based) of this query. Defaults to 0. + Genomic positions are non-negative integers less than reference length. + Requests spanning the join of circular genomes are represented as + two requests one on each side of the join (position 0). */ long start = 0; diff --git a/src/main/resources/avro/variantmethods.avdl b/src/main/resources/avro/variantmethods.avdl index b5720ad5..2cc8abde 100644 --- a/src/main/resources/avro/variantmethods.avdl +++ b/src/main/resources/avro/variantmethods.avdl @@ -71,6 +71,9 @@ record GASearchVariantsRequest { /** Required. The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. + Genomic positions are non-negative integers less than reference length. + Requests spanning the join of circular genomes are represented as + two requests one on each side of the join (position 0). */ long start; diff --git a/src/main/resources/avro/variants.avdl b/src/main/resources/avro/variants.avdl index e268accb..50cfc8f2 100644 --- a/src/main/resources/avro/variants.avdl +++ b/src/main/resources/avro/variants.avdl @@ -182,6 +182,9 @@ record GAVariant { /** The start position at which this variant occurs (0-based). This corresponds to the first base of the string of reference bases. + Genomic positions are non-negative integers less than reference length. + Variants spanning the join of circular genomes are represented as + two variants one on each side of the join (position 0). */ long start; diff --git a/src/main/resources/avro/wip/variationReference.avdl b/src/main/resources/avro/wip/variationReference.avdl index 8e0fc012..3b3d5cfb 100644 --- a/src/main/resources/avro/wip/variationReference.avdl +++ b/src/main/resources/avro/wip/variationReference.avdl @@ -94,6 +94,9 @@ record GASegment { string variantId ; //references an id of a GAVariant int start, end ; // start is 0-based and inclusive, end is exclusive // So start <= x < end if end > start, or end < x <= start if end < start. + // Genomic positions are non-negative integers less than reference length. + // Segments spanning the join of circular genomes are represented as + // two segments, one on each side of the join (position 0). GAVariantSide side ; int length ; // alternative to end // if start == 0 and end == 0 then this is the whole Variant