Merge pull request #158 from pcingola/Circular_genomes

Added comments clarifying how to handle coordinates in circular genomes

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;
 

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;
 

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;
 

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;
 

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;
 

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