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>