Clean up fields and doc in fragment.

adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala

@@ -253,7 +253,7 @@ private[adam] class FastqRecordConverter extends Serializable with Logging {
 
     // build and return record
     Fragment.newBuilder
-      .setReadName(firstReadName)
+      .setName(firstReadName)
       .setAlignments(alignments)
       .build
   }

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SingleReadBucket.scala

@@ -142,20 +142,20 @@ private[adam] case class SingleReadBucket(
 
     // start building fragment
     val builder = Fragment.newBuilder()
-      .setReadName(unionReads.head.getReadName)
+      .setName(unionReads.head.getReadName)
       .setAlignments(seqAsJavaList(allReads.toSeq))
 
     // is an insert size defined for this fragment?
     primaryMapped.headOption
       .foreach(r => {
         Option(r.getInferredInsertSize).foreach(is => {
-          builder.setFragmentSize(is.toInt)
+          builder.setInsertSize(is.toInt)
         })
       })
 
     // set record group name, if known
     Option(unionReads.head.getRecordGroupName)
-      .foreach(n => builder.setRunId(n))
+      .foreach(n => builder.setRecordGroupName(n))
 
     builder.build()
   }

adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala

@@ -270,7 +270,7 @@ class AlignmentRecordConverterSuite extends FunSuite {
         .build())
 
     val fragment = Fragment.newBuilder()
-      .setReadName("testRead")
+      .setName("testRead")
       .setAlignments(seqAsJavaList(alignments))
       .build()
 
@@ -307,7 +307,7 @@ class AlignmentRecordConverterSuite extends FunSuite {
       .setQual("?????*****")
       .build())
     val fragment = Fragment.newBuilder()
-      .setReadName("testRead")
+      .setName("testRead")
       .setAlignments(seqAsJavaList(alignments))
       .build()
 

adam-core/src/test/scala/org/bdgenomics/adam/converters/FastqRecordConverterSuite.scala

@@ -130,7 +130,7 @@ class FastqRecordConverterSuite extends FunSuite with PrivateMethodTester {
   test("testing FastqRecordConverter.convertFragment with valid input") {
     val input = (null, new Text("@read\nATCGA\n+\nabcde\n@read\nTCGAT\n+\n12345"))
     val fragment = converter.convertFragment(input)
-    assert(fragment.getReadName == "read")
+    assert(fragment.getName == "read")
 
     // more detailed testing
     val align1 = fragment.getAlignments.get(0)
@@ -151,7 +151,7 @@ class FastqRecordConverterSuite extends FunSuite with PrivateMethodTester {
   test("testing FastqRecordConverter.convertFragment with another valid input having /1, /2 suffixes") {
     val input = (null, new Text("@read/1\nATCGA\n+\nabcde\n@read/2\nTCGAT\n+\n12345"))
     val fragment = converter.convertFragment(input)
-    assert(fragment.getReadName == "read")
+    assert(fragment.getName == "read")
 
     // more detailed testing
     val align1 = fragment.getAlignments.get(0)

adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala

@@ -64,7 +64,7 @@ object NucleotideContigFragmentRDDSuite extends Serializable {
 
   def fragFn(ncf: NucleotideContigFragment): Fragment = {
     Fragment.newBuilder
-      .setReadName(ncf.getContigName)
+      .setName(ncf.getContigName)
       .build
   }
 

adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala

@@ -67,7 +67,7 @@ object CoverageRDDSuite extends Serializable {
 
   def fragFn(cov: Coverage): Fragment = {
     Fragment.newBuilder
-      .setReadName(cov.contigName)
+      .setName(cov.contigName)
       .build
   }
 

adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala

@@ -59,7 +59,7 @@ object FeatureRDDSuite extends Serializable {
 
   def fragFn(f: Feature): Fragment = {
     Fragment.newBuilder
-      .setReadName(f.getContigName)
+      .setName(f.getContigName)
       .build
   }
 

adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala

@@ -124,7 +124,7 @@ object AlignmentRecordRDDSuite extends Serializable {
 
   def fragFn(r: AlignmentRecord): Fragment = {
     Fragment.newBuilder
-      .setReadName(r.getReadName)
+      .setName(r.getReadName)
       .build
   }
 

adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/BinQualitiesSuite.scala

@@ -177,14 +177,14 @@ class BinQualitiesSuite extends ADAMFunSuite {
     testQuals(newRead.getQual)
 
     val fragment = Fragment.newBuilder
-      .setReadName("testFragment")
+      .setName("testFragment")
       .setAlignments(List(read))
       .build
 
     val newFragment = BinQualities.binFragment(fragment, bins)
 
     assert(newFragment.getAlignments.size === 1)
-    assert(newFragment.getReadName === "testFragment")
+    assert(newFragment.getName === "testFragment")
 
     testQuals(newFragment.getAlignments.head.getQual)
   }

adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/SingleReadBucketSuite.scala

@@ -39,7 +39,7 @@ class SingleReadBucketSuite extends FunSuite {
     val srb = SingleReadBucket(unmapped = reads)
     val fragment = srb.toFragment
     assert(fragment.getAlignments.size === 2)
-    assert(fragment.getReadName === "myRead")
+    assert(fragment.getName === "myRead")
   }
 
   test("convert proper pair to fragment") {
@@ -74,8 +74,8 @@ class SingleReadBucketSuite extends FunSuite {
       .build())
     val srb = SingleReadBucket(primaryMapped = reads)
     val fragment = srb.toFragment
-    assert(fragment.getFragmentSize === 8)
-    assert(fragment.getReadName === "myRead")
+    assert(fragment.getInsertSize === 8)
+    assert(fragment.getName === "myRead")
     assert(fragment.getAlignments.size === 2)
   }
 
@@ -125,8 +125,8 @@ class SingleReadBucketSuite extends FunSuite {
       .build())
     val srb = SingleReadBucket(primaryMapped = reads, secondaryMapped = chimera)
     val fragment = srb.toFragment
-    assert(fragment.getFragmentSize === null)
-    assert(fragment.getReadName === "myRead")
+    assert(fragment.getInsertSize === null)
+    assert(fragment.getName === "myRead")
     assert(fragment.getAlignments.size === 3)
   }
 }

adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala

@@ -66,7 +66,7 @@ object GenotypeRDDSuite extends Serializable {
 
   def fragFn(g: Genotype): Fragment = {
     Fragment.newBuilder
-      .setReadName(g.getContigName)
+      .setName(g.getContigName)
       .build
   }
 

adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala

@@ -70,7 +70,7 @@ object VariantRDDSuite extends Serializable {
 
   def fragFn(v: Variant): Fragment = {
     Fragment.newBuilder
-      .setReadName(v.getContigName)
+      .setName(v.getContigName)
       .build
   }
 

pom.xml

@@ -27,7 +27,7 @@
     <hadoop.version>2.7.5</hadoop.version>
     <hadoop-bam.version>7.9.2</hadoop-bam.version>
     <slf4j.version>1.7.25</slf4j.version>
-    <bdg-formats.version>0.11.3</bdg-formats.version>
+    <bdg-formats.version>0.11.4</bdg-formats.version>
     <bdg-utils.version>0.2.13</bdg-utils.version>
     <htsjdk.version>2.16.1</htsjdk.version>
     <scoverage.plugin.version>1.1.1</scoverage.plugin.version>