Merge pull request #499 from calbach/drop-fragment

Revert "Added Fragment to Reads"

src/main/resources/avro/reads.avdl

@@ -153,18 +153,6 @@ record LinearAlignment {
   array<CigarUnit> cigar = [];
 }
 
-/**
-A fragment represents a contiguous stretch of a DNA or RNA molecule. Reads can
-be associated with a fragment to specify they derive from the same molecule.
-TODO: this Fragment object is essentially unused, and may be removed in a future PR.
-*/
-record Fragment {
-
-  /** The fragment ID. */
-  string id;
-
-}
-
 /**
 Each read alignment describes an alignment with additional information
 about the fragment and the read. A read alignment object is equivalent to a
@@ -190,12 +178,6 @@ record ReadAlignment {
 
   // fragment attributes
 
-  /**
-  The fragment ID that this ReadAlignment belongs to.
-  TODO: this is the only reference to the Fragment object, which may be removed in a future PR.
-  */
-  string fragmentId;
-
   /** The fragment name. Equivalent to QNAME (query template name) in SAM. */
   string fragmentName;