diff --git a/adam-apis/pom.xml b/adam-apis/pom.xml
index 261658d014..4039885eb0 100644
--- a/adam-apis/pom.xml
+++ b/adam-apis/pom.xml
@@ -106,6 +106,7 @@
     <dependency>
       <groupId>org.bdgenomics.bdg-formats</groupId>
       <artifactId>bdg-formats</artifactId>
+      <version>0.7.2-SNAPSHOT</version>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
diff --git a/adam-cli/pom.xml b/adam-cli/pom.xml
index 14242a19df..283a555469 100644
--- a/adam-cli/pom.xml
+++ b/adam-cli/pom.xml
@@ -167,6 +167,7 @@
     <dependency>
       <groupId>org.bdgenomics.bdg-formats</groupId>
       <artifactId>bdg-formats</artifactId>
+      <version>0.7.2-SNAPSHOT</version>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fragments2Reads.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fragments2Reads.scala
index a14bc04153..c26a2b3808 100644
--- a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fragments2Reads.scala
+++ b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fragments2Reads.scala
@@ -54,4 +54,4 @@ class Fragments2Reads(protected val args: Fragments2ReadsArgs) extends BDGSparkC
         SequenceDictionary.empty,
         RecordGroupDictionary.empty)
   }
-}
+}
\ No newline at end of file
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala
index 629ff05579..66f5f25285 100644
--- a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala
+++ b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala
@@ -32,7 +32,7 @@ import org.bdgenomics.adam.models.{
 import org.bdgenomics.adam.projections.{ AlignmentRecordField, Filter }
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
-import org.bdgenomics.adam.rdd.read.MDTagging
+import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, MDTagging }
 import org.bdgenomics.adam.rich.RichVariant
 import org.bdgenomics.formats.avro.AlignmentRecord
 import org.bdgenomics.utils.cli._
@@ -267,7 +267,7 @@ class Transform(protected val args: TransformArgs) extends BDGSparkCommand[Trans
       )
     }
 
-    val aRdd =
+    val aRdd: AlignmentRecordRDD =
       if (args.forceLoadBam) {
         sc.loadBam(args.inputPath)
       } else if (args.forceLoadFastq) {
diff --git a/adam-core/pom.xml b/adam-core/pom.xml
index 6754bb5e54..40a5cc7a6e 100644
--- a/adam-core/pom.xml
+++ b/adam-core/pom.xml
@@ -118,6 +118,7 @@
     <dependency>
       <groupId>org.bdgenomics.bdg-formats</groupId>
       <artifactId>bdg-formats</artifactId>
+      <version>0.7.2-SNAPSHOT</version>
     </dependency>
     <dependency>
       <groupId>commons-io</groupId>
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnowns.scala b/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnowns.scala
index d7ba7392d4..dfddb803ec 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnowns.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnowns.scala
@@ -70,7 +70,7 @@ class ConsensusGeneratorFromKnowns(file: String, @transient sc: SparkContext) ex
     // get region
     val start = reads.map(_.record.getStart).min
     val end = reads.map(_.getEnd).max
-    val refId = reads.head.record.getContig.getContigName
+    val refId = reads.head.record.getContigName
 
     val region = ReferenceRegion(refId, start, end + 1)
 
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReads.scala b/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReads.scala
index 0fbf45ea50..89e0769eee 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReads.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReads.scala
@@ -78,7 +78,7 @@ class ConsensusGeneratorFromReads extends ConsensusGenerator {
         Consensus.generateAlternateConsensus(
           r.getSequence,
           ReferencePosition(
-            r.getContig.getContigName,
+            r.getContigName,
             r.getStart
           ),
           r.samtoolsCigar
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
index a7bc70900c..0f39758a3b 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/converters/AlignmentRecordConverter.scala
@@ -118,8 +118,7 @@ class AlignmentRecordConverter extends Serializable {
       })
 
     // set the reference name, and alignment position, for mate
-    Option(adamRecord.getMateContig)
-      .map(_.getContigName)
+    Option(adamRecord.getMateContigName)
       .foreach(builder.setMateReferenceName)
     Option(adamRecord.getMateAlignmentStart)
       .foreach(s => builder.setMateAlignmentStart(s.toInt + 1))
@@ -155,8 +154,8 @@ class AlignmentRecordConverter extends Serializable {
         // only set alignment flags if read is aligned
         if (m) {
           // if we are aligned, we must have a reference
-          assert(adamRecord.getContig != null, "Cannot have null contig if aligned.")
-          builder.setReferenceName(adamRecord.getContig.getContigName)
+          assert(adamRecord.getContigName != null, "Cannot have null contig if aligned.")
+          builder.setReferenceName(adamRecord.getContigName)
 
           // set the cigar, if provided
           Option(adamRecord.getCigar).foreach(builder.setCigarString)
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/FragmentConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/FragmentConverter.scala
index b0d8b1d8e2..6583de2438 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/converters/FragmentConverter.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/converters/FragmentConverter.scala
@@ -93,7 +93,7 @@ object FragmentConverter extends Serializable {
 
       // build record
       AlignmentRecord.newBuilder()
-        .setContig(contig)
+        .setContigName(contig.getContigName)
         .setStart(fragmentRegion.start)
         .setEnd(fragmentRegion.end)
         .setSequence(fragmentString)
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala
index afec7c03b6..a4456187b2 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala
@@ -81,7 +81,7 @@ class SAMRecordConverter extends Serializable with Logging {
       val readReference: Int = samRecord.getReferenceIndex
       if (readReference != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
         dict(samRecord.getReferenceName).foreach { (rec) =>
-          builder.setContig(SequenceRecord.toADAMContig(rec))
+          builder.setContigName(SequenceRecord.toADAMContig(rec).getContigName)
         }
 
         // set read alignment flag
@@ -128,7 +128,7 @@ class SAMRecordConverter extends Serializable with Logging {
 
       if (mateReference != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
         dict(samRecord.getMateReferenceName).foreach { (rec) =>
-          builder.setMateContig(SequenceRecord.toADAMContig(rec))
+          builder.setMateContigName(SequenceRecord.toADAMContig(rec).getContigName)
         }
 
         val mateStart = samRecord.getMateAlignmentStart
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
index db2598df6d..7c57a10b62 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala
@@ -49,7 +49,7 @@ object ReferencePosition extends Serializable {
    * @see fivePrime
    */
   def apply(record: AlignmentRecord): ReferencePosition = {
-    new ReferencePosition(record.getContig.getContigName, record.getStart)
+    new ReferencePosition(record.getContigName, record.getStart)
   }
 
   /**
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
index f3d042ed4a..75906a7f8e 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala
@@ -82,7 +82,7 @@ object ReferenceRegion {
     if (record.getReadMapped) {
       Some(
         ReferenceRegion(
-          record.getContig.getContigName,
+          record.getContigName,
           record.getStart,
           record.getEnd
         )
@@ -92,7 +92,7 @@ object ReferenceRegion {
   }
 
   def apply(record: AlignmentRecord): ReferenceRegion = {
-    ReferenceRegion(record.getContig.getContigName, record.getStart, record.getEnd)
+    ReferenceRegion(record.getContigName, record.getStart, record.getEnd)
   }
 
   /**
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala b/adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
index d26ee46a1c..205e44975c 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala
@@ -345,27 +345,6 @@ object SequenceRecord {
     fromADAMContig(fragment.getContig)
   }
 
-  /**
-   * Convert an Read into one or more SequenceRecords.
-   * The reason that we can't simply use the "fromSpecificRecord" method, below, is that each Read
-   * can (through the fact that it could be a pair of reads) contain 1 or 2 possible SequenceRecord entries
-   * for the SequenceDictionary itself.  Both have to be extracted, separately.
-   *
-   * @param rec The Read from which to extract the SequenceRecord entries
-   * @return a list of all SequenceRecord entries derivable from this record.
-   */
-  def fromADAMRecord(rec: AlignmentRecord): Set[SequenceRecord] = {
-    assert(rec != null, "Read was null")
-    if (rec.getContig != null || rec.getMateContig != null) {
-      // The contig should be null for unmapped read
-      List(Option(rec.getContig), Option(rec.getMateContig))
-        .flatten
-        .map(fromADAMContig)
-        .toSet
-    } else
-      Set()
-  }
-
   def fromSpecificRecord(rec: IndexedRecord): SequenceRecord = {
     val schema = rec.getSchema
     if (schema.getField("referenceId") != null) {
@@ -381,4 +360,6 @@ object SequenceRecord {
       throw new AssertionError("Missing information to generate SequenceRecord")
     }
   }
+
 }
+
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
index f9db02e13d..8f58ccdd08 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
@@ -229,9 +229,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
       val projected: RDD[T] = loadParquet[T](filePath, None, projection = Some(projection))
 
       val recs: RDD[SequenceRecord] =
-        if (isADAMRecord) {
-          projected.asInstanceOf[RDD[AlignmentRecord]].distinct().flatMap(rec => SequenceRecord.fromADAMRecord(rec))
-        } else if (isADAMContig) {
+        if (isADAMContig) {
           projected.asInstanceOf[RDD[NucleotideContigFragment]].distinct().map(ctg => SequenceRecord.fromADAMContigFragment(ctg))
         } else {
           projected.distinct().map(SequenceRecord.fromSpecificRecord(_))
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDFunctions.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDFunctions.scala
index dc46354220..e090ec2057 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDFunctions.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDFunctions.scala
@@ -21,18 +21,14 @@ import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.converters.AlignmentRecordConverter
 import org.bdgenomics.adam.models.SequenceRecord
 import org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator
+import org.apache.spark.Logging
 import org.bdgenomics.formats.avro._
 import scala.collection.JavaConversions._
 
-class FragmentRDDFunctions(rdd: RDD[Fragment]) extends ADAMSequenceDictionaryRDDAggregator[Fragment](rdd) {
+class FragmentRDDFunctions(rdd: RDD[Fragment]) extends Serializable with Logging {
 
   def toReads: RDD[AlignmentRecord] = {
     val converter = new AlignmentRecordConverter
     rdd.flatMap(converter.convertFragment)
   }
-
-  def getSequenceRecordsFromElement(elem: Fragment): Set[SequenceRecord] = {
-    val alignments = asScalaBuffer(elem.getAlignments)
-    alignments.flatMap(SequenceRecord.fromADAMRecord).toSet
-  }
 }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala
index b39d4319e1..b70efc3d47 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala
@@ -32,7 +32,7 @@ import org.apache.avro.specific.{ SpecificDatumWriter, SpecificRecordBase }
 import org.apache.hadoop.conf.Configuration
 import org.apache.hadoop.fs.{ FileSystem, FileUtil, Path }
 import org.apache.hadoop.io.LongWritable
-import org.apache.spark.SparkContext
+import org.apache.spark.{ Logging, SparkContext }
 import org.apache.spark.broadcast.Broadcast
 import org.apache.spark.rdd.MetricsContext._
 import org.apache.spark.rdd.RDD
@@ -53,9 +53,7 @@ import scala.annotation.tailrec
 import scala.language.implicitConversions
 import scala.reflect.ClassTag
 
-class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
-    extends ADAMSequenceDictionaryRDDAggregator[AlignmentRecord](rdd) {
-
+class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord]) extends Serializable with Logging {
   /**
    * Calculates the subset of the RDD whose AlignmentRecords overlap the corresponding
    * query ReferenceRegion.  Equality of the reference sequence (to which these are aligned)
@@ -72,7 +70,7 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
   def filterByOverlappingRegion(query: ReferenceRegion): RDD[AlignmentRecord] = {
     def overlapsQuery(rec: AlignmentRecord): Boolean =
       rec.getReadMapped &&
-        rec.getContig.getContigName == query.referenceName &&
+        rec.getContigName == query.referenceName &&
         rec.getStart < query.end &&
         rec.getEnd > query.start
     rdd.filter(overlapsQuery)
@@ -126,7 +124,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    * As such, we must force the user to pass in the schema.
    *
    * @tparam T The type of the specific record we are saving.
-   *
    * @param filename Path to save records to.
    * @param sc SparkContext used for identifying underlying file system.
    * @param schema Schema of records we are saving.
@@ -171,7 +168,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    *   aligned to.
    * @param rgd Record group dictionary describing the record groups these
    *   reads are from.
-   *
    * @see adamSave
    * @see adamAlignedRecordSave
    */
@@ -212,7 +208,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    *   aligned to.
    * @param rgd Record group dictionary describing the record groups these
    *   reads are from.
-   *
    * @see adamSave
    * @see adamSAMSave
    * @see saveAsParquet
@@ -235,7 +230,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    *   aligned to.
    * @param rgd Record group dictionary describing the record groups these
    *   reads are from.
-   *
    * @see adamAlignedRecordSave
    * @see adamSAMSave
    * @see saveAsParquet
@@ -263,9 +257,7 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    *   aligned to.
    * @param rgd Record group dictionary describing the record groups these
    *   reads are from.
-   *
    * @return A string on the driver representing this RDD of reads in SAM format.
-   *
    * @see adamConvertToSAM
    */
   def adamSAMString(sd: SequenceDictionary,
@@ -593,10 +585,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
     }
   }
 
-  def getSequenceRecordsFromElement(elem: AlignmentRecord): Set[SequenceRecord] = {
-    SequenceRecord.fromADAMRecord(elem).toSet
-  }
-
   /**
    * Converts an RDD of ADAM read records into SAM records.
    *
@@ -635,7 +623,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    *
    * @param kmerLength The value of _k_ to use for cutting _k_-mers.
    * @return Returns an RDD containing k-mer/count pairs.
-   *
    * @see adamCountQmers
    */
   def adamCountKmers(kmerLength: Int): RDD[(String, Long)] = {
@@ -696,7 +683,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    * Realigns indels using a concensus-based heuristic.
    *
    * @see RealignIndels
-   *
    * @param isSorted If the input data is sorted, setting this parameter to true avoids a second sort.
    * @param maxIndelSize The size of the largest indel to use for realignment.
    * @param maxConsensusNumber The maximum number of consensus sequences to realign against per
@@ -704,7 +690,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    * @param lodThreshold Log-odds threhold to use when realigning; realignments are only finalized
    * if the log-odds threshold is exceeded.
    * @param maxTargetSize The maximum width of a single target region for realignment.
-   *
    * @return Returns an RDD of mapped reads which have been realigned.
    */
   def adamRealignIndels(
@@ -724,6 +709,7 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
 
   /**
    * Groups all reads by record group and read name
+   *
    * @return SingleReadBuckets with primary, secondary and unmapped reads
    */
   def adamSingleReadBuckets(): RDD[SingleReadBucket] = {
@@ -759,6 +745,7 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
 
   /**
    * Returns the subset of the ADAMRecords which have an attribute with the given name.
+   *
    * @param tagName The name of the attribute to filter on (should be length 2)
    * @return An RDD[Read] containing the subset of records with a tag that matches the given name.
    */
@@ -928,7 +915,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
    * were _originally_ paired together.
    *
    * @note The RDD that this is called on should be the RDD with the first read from the pair.
-   *
    * @param secondPairRdd The rdd containing the second read from the pairs.
    * @param validationStringency How stringently to validate the reads.
    * @return Returns an RDD with the pair information recomputed.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala
index 6fcc690fb4..d2151480ef 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala
@@ -44,7 +44,7 @@ object DuplicateMetrics {
         b2i(f(record)),
         b2i(f(record) && record.getReadMapped && record.getMateMapped),
         b2i(f(record) && record.getReadMapped && !record.getMateMapped),
-        b2i(f(record) && (!isSameContig(record.getContig, record.getMateContig)))
+        b2i(f(record) && (!isSameContig(record.getContigName, record.getMateContigName)))
       )
     }
     (duplicateMetrics(isPrimary), duplicateMetrics(isSecondary))
@@ -97,7 +97,7 @@ object FlagStat {
     rdd.map {
       p =>
         val mateMappedToDiffChromosome =
-          p.getReadPaired && p.getReadMapped && p.getMateMapped && !isSameContig(p.getContig, p.getMateContig)
+          p.getReadPaired && p.getReadMapped && p.getMateMapped && !isSameContig(p.getContigName, p.getMateContigName)
         val (primaryDuplicates, secondaryDuplicates) = DuplicateMetrics(p)
         new FlagStatMetrics(
           1,
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
index 0d86459650..9f171c287c 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
@@ -72,8 +72,7 @@ case class MDTagging(
     val referenceFileB = sc.broadcast(referenceFile)
     reads.map(read => {
       (for {
-        contig <- Option(read.getContig)
-        contigName <- Option(contig.getContigName)
+        contig <- Option(read.getContigName)
         if read.getReadMapped
       } yield {
         maybeMDTagRead(read, referenceFileB.value.extract(ReferenceRegion(read)))
@@ -105,5 +104,5 @@ object MDTagging {
 
 case class IncorrectMDTagException(read: AlignmentRecord, mdTag: String) extends Exception {
   override def getMessage: String =
-    s"Read: ${read.getReadName}, pos: ${read.getContig.getContigName}:${read.getStart}, cigar: ${read.getCigar}, existing MD tag: ${read.getMismatchingPositions}, correct MD tag: $mdTag"
+    s"Read: ${read.getReadName}, pos: ${read.getContigName}:${read.getStart}, cigar: ${read.getCigar}, existing MD tag: ${read.getMismatchingPositions}, correct MD tag: $mdTag"
 }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
index c20f6ed386..e0c1b440ad 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
@@ -102,7 +102,7 @@ object IndelRealignmentTarget {
     maxIndelSize: Int): Seq[IndelRealignmentTarget] = CreateIndelRealignmentTargets.time {
 
     val region = ReferenceRegion(read.record)
-    val refId = read.record.getContig.getContigName
+    val refId = read.record.getContigName
     var pos = List[ReferenceRegion]()
     var referencePos = read.record.getStart
     val cigar = read.samtoolsCigar
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
index d0995d8fd1..d98d6101c5 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
@@ -251,7 +251,7 @@ private[rdd] class RealignIndels(
 
       // get reference from reads
       val (reference, refStart, refEnd) = getReferenceFromReads(reads.map(r => new RichAlignmentRecord(r)))
-      val refRegion = ReferenceRegion(reads.head.record.getContig.getContigName, refStart, refEnd)
+      val refRegion = ReferenceRegion(reads.head.record.getContigName, refStart, refEnd)
 
       // preprocess reads and get consensus
       val readsToClean = consensusModel.preprocessReadsForRealignment(
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichAlignmentRecord.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichAlignmentRecord.scala
index e6bcf46eac..3f07fdfd27 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichAlignmentRecord.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichAlignmentRecord.scala
@@ -132,7 +132,7 @@ class RichAlignmentRecord(val record: AlignmentRecord) {
       } else {
         Strand.Forward
       }
-      ReferencePosition(record.getContig.getContigName, fivePrimePosition, strand)
+      ReferencePosition(record.getContigName, fivePrimePosition, strand)
     } catch {
       case e: Throwable => {
         println("caught " + e + " when trying to get position for " + record)
@@ -167,7 +167,7 @@ class RichAlignmentRecord(val record: AlignmentRecord) {
 
   def getReferenceContext(readOffset: Int, referencePosition: Long, cigarElem: CigarElement, elemOffset: Int): ReferenceSequenceContext = {
     val position = if (record.getReadMapped) {
-      Some(ReferencePosition(record.getContig.getContigName, referencePosition))
+      Some(ReferencePosition(record.getContigName, referencePosition))
     } else {
       None
     }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/util/Util.scala b/adam-core/src/main/scala/org/bdgenomics/adam/util/Util.scala
index c918dcb711..57f2bbf728 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/util/Util.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/util/Util.scala
@@ -16,9 +16,13 @@
  * limitations under the License.
  */
 package org.bdgenomics.adam.util
-
 import org.bdgenomics.formats.avro.Contig
 
+// We may want to reintroduce in the future MD5 concordance test for isSameContig as
+// was dpne previously in the  commented out code below
+// With change to factoring Contig out of AlignmentRecord it was most
+// straightforward to simply check for contig name equivalence for now
+/*
 object Util {
   def isSameContig(left: Contig, right: Contig): Boolean = {
     val leftName = Option(left).map(_.getContigName)
@@ -27,4 +31,11 @@ object Util {
     val rightMD5 = Option(right).map(_.getContigMD5)
     leftName == rightName && (leftMD5.isEmpty || rightMD5.isEmpty || leftMD5 == rightMD5)
   }
+*/
+
+object Util {
+  def isSameContig(left: String, right: String): Boolean = {
+    left == right
+  }
+
 }
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala
index e0ff82056b..c106d4f958 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala
@@ -66,14 +66,8 @@ class AlignmentRecordConverterSuite extends FunSuite {
     // add reference details
     adamRead.setRecordGroupName("record_group")
     adamRead.setRecordGroupSample("sample")
-    adamRead.setContig(Contig.newBuilder()
-      .setContigName("referencetest")
-      .build())
-    adamRead.setMateContig(Contig.newBuilder()
-      .setContigName("matereferencetest")
-      .setContigLength(6L)
-      .setReferenceURL("test://chrom1")
-      .build())
+    adamRead.setContigName("referencetest")
+    adamRead.setMateContigName("matereferencetest")
     adamRead.setMateAlignmentStart(6L)
 
     // make sequence dictionary
@@ -115,14 +109,8 @@ class AlignmentRecordConverterSuite extends FunSuite {
     // add reference details
     adamRead.setRecordGroupName("record_group")
     adamRead.setRecordGroupSample("sample")
-    adamRead.setContig(Contig.newBuilder()
-      .setContigName("referencetest")
-      .build())
-    adamRead.setMateContig(Contig.newBuilder()
-      .setContigName("matereferencetest")
-      .setContigLength(6L)
-      .setReferenceURL("test://chrom1")
-      .build())
+    adamRead.setContigName("referencetest")
+    adamRead.setMateContigName("matereferencetest")
     adamRead.setMateAlignmentStart(6L)
 
     // make sequence dictionary
@@ -312,9 +300,7 @@ class AlignmentRecordConverterSuite extends FunSuite {
   test("converting a fragment with alignments should restore the alignments") {
     val alignments = List(AlignmentRecord.newBuilder()
       .setReadMapped(true)
-      .setContig(Contig.newBuilder()
-        .setContigName("1")
-        .build())
+      .setContigName("1")
       .setStart(10L)
       .setEnd(20L)
       .setReadName("testRead")
@@ -341,7 +327,7 @@ class AlignmentRecordConverterSuite extends FunSuite {
     assert(read.getCigar === "10M")
     assert(read.getSequence === "TACTGTGGGT")
     assert(read.getQual === "?????*****")
-    assert(read.getContig.getContigName === "1")
+    assert(read.getContigName === "1")
   }
 }
 
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/converters/FragmentConverterSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/converters/FragmentConverterSuite.scala
index d52e687e68..c72913e645 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/converters/FragmentConverterSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/converters/FragmentConverterSuite.scala
@@ -41,7 +41,7 @@ class FragmentConverterSuite extends ADAMFunSuite {
     val convertedRead = convertedReads.head
 
     assert(convertedRead.getSequence === "ACACACAC")
-    assert(convertedRead.getContig.getContigName === "ctg")
+    assert(convertedRead.getContigName === "ctg")
     assert(convertedRead.getStart === 0L)
     assert(convertedRead.getEnd === 8L)
   }
@@ -65,11 +65,11 @@ class FragmentConverterSuite extends ADAMFunSuite {
     val secondRead = reads.filter(_.getStart != 0L).head
 
     assert(firstRead.getSequence === "ACACACAC")
-    assert(firstRead.getContig.getContigName === "ctg")
+    assert(firstRead.getContigName === "ctg")
     assert(firstRead.getStart === 0L)
     assert(firstRead.getEnd === 8L)
     assert(secondRead.getSequence === "AATTCCGGCCTTAA")
-    assert(secondRead.getContig.getContigName === "ctg")
+    assert(secondRead.getContigName === "ctg")
     assert(secondRead.getStart === 14L)
     assert(secondRead.getEnd === 28L)
   }
@@ -95,7 +95,7 @@ class FragmentConverterSuite extends ADAMFunSuite {
     assert(reads.length === 1)
     val read = reads(0)
     assert(read.getSequence === "ACACACACTGTGTGAATTCCGGCCTTAA")
-    assert(read.getContig.getContigName === "ctg")
+    assert(read.getContigName === "ctg")
     assert(read.getStart === 0L)
     assert(read.getEnd === 28L)
   }
@@ -132,36 +132,36 @@ class FragmentConverterSuite extends ADAMFunSuite {
 
     assert(reads.length === 4)
 
-    val ctg1Reads = reads.filter(_.getContig.getContigName == "ctg1")
+    val ctg1Reads = reads.filter(_.getContigName == "ctg1")
     assert(ctg1Reads.length === 1)
 
     val ctg1Read = ctg1Reads.head
     assert(ctg1Read.getSequence === "ACACACACTGTGTGAATTCCGGCCTTAA")
-    assert(ctg1Read.getContig.getContigName === "ctg1")
+    assert(ctg1Read.getContigName === "ctg1")
     assert(ctg1Read.getStart === 0L)
     assert(ctg1Read.getEnd === 28L)
 
-    val ctg2Reads = reads.filter(_.getContig.getContigName == "ctg2")
+    val ctg2Reads = reads.filter(_.getContigName == "ctg2")
     assert(ctg2Reads.length === 2)
 
     val firstCtg2Read = ctg2Reads.filter(_.getStart == 0L).head
     val secondCtg2Read = ctg2Reads.filter(_.getStart != 0L).head
 
     assert(firstCtg2Read.getSequence === "ACACACAC")
-    assert(firstCtg2Read.getContig.getContigName === "ctg2")
+    assert(firstCtg2Read.getContigName === "ctg2")
     assert(firstCtg2Read.getStart === 0L)
     assert(firstCtg2Read.getEnd === 8L)
     assert(secondCtg2Read.getSequence === "AATTCCGGCCTTAA")
-    assert(secondCtg2Read.getContig.getContigName === "ctg2")
+    assert(secondCtg2Read.getContigName === "ctg2")
     assert(secondCtg2Read.getStart === 14L)
     assert(secondCtg2Read.getEnd === 28L)
 
-    val ctg3Reads = reads.filter(_.getContig.getContigName == "ctg3")
+    val ctg3Reads = reads.filter(_.getContigName == "ctg3")
     assert(ctg3Reads.length === 1)
 
     val ctg3Read = ctg3Reads.head
     assert(ctg3Read.getSequence === "AATTCCGGCCTTAA")
-    assert(ctg3Read.getContig.getContigName === "ctg3")
+    assert(ctg3Read.getContigName === "ctg3")
     assert(ctg3Read.getStart === 14L)
     assert(ctg3Read.getEnd === 28L)
   }
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferencePositionSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferencePositionSuite.scala
index b2c35c66d2..8fdae451b6 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferencePositionSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferencePositionSuite.scala
@@ -28,7 +28,7 @@ class ReferencePositionSuite extends FunSuite {
       .build
 
     val read = AlignmentRecord.newBuilder()
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .build()
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala
index 8afd815bd7..b0bd31c5d0 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/models/ReferenceRegionSuite.scala
@@ -137,10 +137,7 @@ class ReferenceRegionSuite extends FunSuite {
       .setStart(1L)
       .setCigar("5M")
       .setEnd(6L)
-      .setContig(Contig.newBuilder
-        .setContigName("chr1")
-        .setContigLength(10L)
-        .build)
+      .setContigName("chr1")
       .build()
 
     assert(ReferenceRegion(read).contains(point("chr1", 1L)))
@@ -192,7 +189,7 @@ class ReferenceRegionSuite extends FunSuite {
     val read = AlignmentRecord.newBuilder()
       .setStart(5L)
       .setSequence("ACGT")
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setReadMapped(true)
       .setCigar("5M")
       .setEnd(10L)
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/models/SingleReadBucketSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/models/SingleReadBucketSuite.scala
index 72ef98d5d0..758872b7a6 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/models/SingleReadBucketSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/models/SingleReadBucketSuite.scala
@@ -53,9 +53,7 @@ class SingleReadBucketSuite extends FunSuite {
       .setPrimaryAlignment(true)
       .setReadNegativeStrand(false)
       .setCigar("8M")
-      .setContig(Contig.newBuilder()
-        .setContigName("1")
-        .build())
+      .setContigName("1")
       .setStart(10L)
       .setEnd(18L)
       .setInferredInsertSize(8L)
@@ -69,9 +67,7 @@ class SingleReadBucketSuite extends FunSuite {
       .setPrimaryAlignment(true)
       .setReadNegativeStrand(true)
       .setCigar("8M")
-      .setContig(Contig.newBuilder()
-        .setContigName("1")
-        .build())
+      .setContigName("1")
       .setStart(22L)
       .setEnd(30L)
       .setInferredInsertSize(8L)
@@ -95,9 +91,7 @@ class SingleReadBucketSuite extends FunSuite {
       .setPrimaryAlignment(true)
       .setCigar("8M6H")
       .setBasesTrimmedFromEnd(6)
-      .setContig(Contig.newBuilder()
-        .setContigName("1")
-        .build())
+      .setContigName("1")
       .setStart(10L)
       .setEnd(18L)
       .build(), AlignmentRecord.newBuilder()
@@ -110,9 +104,7 @@ class SingleReadBucketSuite extends FunSuite {
       .setPrimaryAlignment(true)
       .setReadNegativeStrand(true)
       .setCigar("8M")
-      .setContig(Contig.newBuilder()
-        .setContigName("1")
-        .build())
+      .setContigName("1")
       .setStart(22L)
       .setEnd(30L)
       .build())
@@ -127,9 +119,7 @@ class SingleReadBucketSuite extends FunSuite {
       .setSupplementaryAlignment(true)
       .setBasesTrimmedFromStart(8)
       .setCigar("8H6M")
-      .setContig(Contig.newBuilder()
-        .setContigName("2")
-        .build())
+      .setContigName("2")
       .setStart(100L)
       .setEnd(106L)
       .build())
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
index 4eea2176c8..0c9185e6c9 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
@@ -165,7 +165,7 @@ class ADAMContextSuite extends ADAMFunSuite {
     val a0 = AlignmentRecord.newBuilder()
       .setRecordGroupName("group0")
       .setReadName("read0")
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setStart(100)
       .setPrimaryAlignment(true)
       .setReadPaired(false)
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/BroadcastRegionJoinSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/BroadcastRegionJoinSuite.scala
index 76fc5a2070..4e77e31ab4 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/BroadcastRegionJoinSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/BroadcastRegionJoinSuite.scala
@@ -90,7 +90,7 @@ class BroadcastRegionJoinSuite extends ADAMFunSuite {
       .build
 
     val built = AlignmentRecord.newBuilder()
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
@@ -117,7 +117,7 @@ class BroadcastRegionJoinSuite extends ADAMFunSuite {
       .build
 
     val builder = AlignmentRecord.newBuilder()
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
@@ -154,7 +154,7 @@ class BroadcastRegionJoinSuite extends ADAMFunSuite {
       .build
 
     val built = AlignmentRecord.newBuilder()
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
@@ -194,14 +194,14 @@ class BroadcastRegionJoinSuite extends ADAMFunSuite {
       .build
 
     val builtRef1 = AlignmentRecord.newBuilder()
-      .setContig(contig1)
+      .setContigName(contig1.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
       .setEnd(2L)
       .build()
     val builtRef2 = AlignmentRecord.newBuilder()
-      .setContig(contig2)
+      .setContigName(contig2.getContigName)
       .setStart(1)
       .setReadMapped(true)
       .setCigar("1M")
@@ -243,14 +243,14 @@ class BroadcastRegionJoinSuite extends ADAMFunSuite {
       .build
 
     val builtRef1 = AlignmentRecord.newBuilder()
-      .setContig(contig1)
+      .setContigName(contig1.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
       .setEnd(2L)
       .build()
     val builtRef2 = AlignmentRecord.newBuilder()
-      .setContig(contig2)
+      .setContigName(contig2.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicPositionPartitionerSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicPositionPartitionerSuite.scala
index d221930a8c..cffe849d4b 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicPositionPartitionerSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicPositionPartitionerSuite.scala
@@ -82,7 +82,7 @@ class GenomicPositionPartitionerSuite extends ADAMFunSuite {
     val count = 1000
     val pos = sc.parallelize((1 to count).map(i => adamRecord("chr1", "read_%d".format(i), rand.nextInt(100), readMapped = true)), 1)
     val parts = 200
-    val pairs = pos.map(p => (ReferencePosition(p.getContig.getContigName, p.getStart), p))
+    val pairs = pos.map(p => (ReferencePosition(p.getContigName, p.getStart), p))
     val parter = new RangePartitioner(parts, pairs)
     val partitioned = pairs.sortByKey().partitionBy(parter)
 
@@ -109,7 +109,7 @@ class GenomicPositionPartitionerSuite extends ADAMFunSuite {
     assert(rdd.count() === 200)
 
     val keyed =
-      rdd.map(rec => (ReferencePosition(rec.getContig.getContigName, rec.getStart), rec)).sortByKey()
+      rdd.map(rec => (ReferencePosition(rec.getContigName, rec.getStart), rec)).sortByKey()
 
     val keys = keyed.map(_._1).collect()
     assert(!keys.exists(rp => parter.getPartition(rp) < 0 || parter.getPartition(rp) >= parts))
@@ -131,7 +131,7 @@ class GenomicPositionPartitionerSuite extends ADAMFunSuite {
       .build
 
     AlignmentRecord.newBuilder()
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setReadName(readName)
       .setReadMapped(readMapped)
       .setStart(start)
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoinSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoinSuite.scala
index f13adcf329..283c13191a 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoinSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoinSuite.scala
@@ -40,7 +40,7 @@ class ShuffleRegionJoinSuite extends ADAMFunSuite {
       .build
 
     val built = AlignmentRecord.newBuilder()
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
@@ -90,14 +90,14 @@ class ShuffleRegionJoinSuite extends ADAMFunSuite {
       .build
 
     val builtRef1 = AlignmentRecord.newBuilder()
-      .setContig(contig1)
+      .setContigName(contig1.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
       .setEnd(2L)
       .build()
     val builtRef2 = AlignmentRecord.newBuilder()
-      .setContig(contig2)
+      .setContigName(contig2.getContigName)
       .setStart(1)
       .setReadMapped(true)
       .setCigar("1M")
@@ -149,14 +149,14 @@ class ShuffleRegionJoinSuite extends ADAMFunSuite {
       .build
 
     val builtRef1 = AlignmentRecord.newBuilder()
-      .setContig(contig1)
+      .setContigName(contig1.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
       .setEnd(2L)
       .build()
     val builtRef2 = AlignmentRecord.newBuilder()
-      .setContig(contig2)
+      .setContigName(contig2.getContigName)
       .setStart(1L)
       .setReadMapped(true)
       .setCigar("1M")
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctionsSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctionsSuite.scala
index 32c3b7a2f7..6a2a2e2b0b 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctionsSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctionsSuite.scala
@@ -41,7 +41,7 @@ class AlignmentRecordRDDFunctionsSuite extends ADAMFunSuite {
           .setContigName(random.nextInt(numReadsToCreate / 10).toString)
           .build
         val start = random.nextInt(1000000)
-        builder.setContig(contig).setStart(start).setEnd(start)
+        builder.setContigName(contig.getContigName).setStart(start).setEnd(start)
       }
       builder.setReadName((0 until 20).map(i => (random.nextInt(100) + 64)).mkString)
       builder.build()
@@ -53,7 +53,7 @@ class AlignmentRecordRDDFunctionsSuite extends ADAMFunSuite {
     assert(unmapped.forall(p => p._2 > mapped.takeRight(1)(0)._2))
     // Make sure that we appropriately sorted the reads
     val expectedSortedReads = mapped.sortWith(
-      (a, b) => a._1.getContig.getContigName.toString < b._1.getContig.getContigName.toString && a._1.getStart < b._1.getStart)
+      (a, b) => a._1.getContigName.toString < b._1.getContigName.toString && a._1.getStart < b._1.getStart)
     assert(expectedSortedReads === mapped)
   }
 
@@ -350,7 +350,7 @@ class AlignmentRecordRDDFunctionsSuite extends ADAMFunSuite {
         // that some fields should be disregarded if the read is not mapped
         if (p1.getReadMapped && p2.getReadMapped) {
           assert(p1.getDuplicateRead === p2.getDuplicateRead)
-          assert(p1.getContig.getContigName === p2.getContig.getContigName)
+          assert(p1.getContigName === p2.getContigName)
           assert(p1.getStart === p2.getStart)
           assert(p1.getEnd === p2.getEnd)
           assert(p1.getCigar === p2.getCigar)
@@ -371,7 +371,7 @@ class AlignmentRecordRDDFunctionsSuite extends ADAMFunSuite {
           assert(p1.getMateMapped === p2.getMateMapped)
           if (p1.getMateMapped && p2.getMateMapped) {
             assert(p1.getMateNegativeStrand === p2.getMateNegativeStrand)
-            assert(p1.getMateContig.getContigName === p2.getMateContig.getContigName)
+            assert(p1.getMateContigName === p2.getMateContigName)
             assert(p1.getMateAlignmentStart === p2.getMateAlignmentStart)
             assert(p1.getMateAlignmentEnd === p2.getMateAlignmentEnd)
           }
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MDTaggingSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MDTaggingSuite.scala
index e6c0929b82..840c35b764 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MDTaggingSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MDTaggingSuite.scala
@@ -45,7 +45,7 @@ class MDTaggingSuite extends ADAMFunSuite {
         id -> mdTag,
         AlignmentRecord
         .newBuilder
-        .setContig(contig)
+        .setContigName(contig.getContigName)
         .setStart(start.toLong)
         .setEnd(end.toLong)
         .setSequence(seq)
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MarkDuplicatesSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MarkDuplicatesSuite.scala
index 2f68b8bbfb..6fab0b1676 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MarkDuplicatesSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MarkDuplicatesSuite.scala
@@ -49,7 +49,7 @@ class MarkDuplicatesSuite extends ADAMFunSuite {
       .build
 
     AlignmentRecord.newBuilder()
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setStart(start)
       .setQual(qual)
       .setCigar(cigar)
@@ -79,14 +79,14 @@ class MarkDuplicatesSuite extends ADAMFunSuite {
       readName = readName, avgPhredScore = avgPhredScore)
     firstOfPair.setReadInFragment(0)
     firstOfPair.setMateMapped(true)
-    firstOfPair.setMateContig(secondContig)
+    firstOfPair.setMateContigName(secondContig.getContigName)
     firstOfPair.setMateAlignmentStart(secondStart)
     firstOfPair.setReadPaired(true)
     val secondOfPair = createMappedRead(secondReferenceName, secondStart, secondEnd,
       readName = readName, avgPhredScore = avgPhredScore, isNegativeStrand = true)
     secondOfPair.setReadInFragment(1)
     secondOfPair.setMateMapped(true)
-    secondOfPair.setMateContig(firstContig)
+    secondOfPair.setMateContigName(firstContig.getContigName)
     secondOfPair.setMateAlignmentStart(firstStart)
     secondOfPair.setReadPaired(true)
     Seq(firstOfPair, secondOfPair)
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala
index 04b34719bc..e158128afa 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala
@@ -49,9 +49,7 @@ class IndelRealignmentTargetSuite extends ADAMFunSuite {
       .setReadNegativeStrand(false)
       .setMapq(60)
       .setQual(sequence) // no typo, we just don't care
-      .setContig(Contig.newBuilder()
-        .setContigName("1")
-        .build())
+      .setContigName("1")
       .setMismatchingPositions(mdtag)
       .build())
   }
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala
index c1ed855105..63d0477b85 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala
@@ -182,7 +182,7 @@ class RealignIndelsSuite extends ADAMFunSuite {
       .setContigName("chr1")
       .build()
     val reads = Seq(AlignmentRecord.newBuilder()
-      .setContig(ctg)
+      .setContigName(ctg.getContigName)
       .setStart(1L)
       .setEnd(4L)
       .setSequence("AAA")
@@ -191,7 +191,7 @@ class RealignIndelsSuite extends ADAMFunSuite {
       .setReadMapped(true)
       .setMismatchingPositions("3")
       .build(), AlignmentRecord.newBuilder()
-      .setContig(ctg)
+      .setContigName(ctg.getContigName)
       .setStart(9L)
       .setEnd(12L)
       .setSequence("AAA")
@@ -213,7 +213,7 @@ class RealignIndelsSuite extends ADAMFunSuite {
       .setContigName("chr1")
       .build()
     val reads = sc.parallelize(Seq(AlignmentRecord.newBuilder()
-      .setContig(ctg)
+      .setContigName(ctg.getContigName)
       .setStart(1L)
       .setEnd(4L)
       .setSequence("AAA")
@@ -222,7 +222,7 @@ class RealignIndelsSuite extends ADAMFunSuite {
       .setReadMapped(true)
       .setMismatchingPositions("3")
       .build(), AlignmentRecord.newBuilder()
-      .setContig(ctg)
+      .setContigName(ctg.getContigName)
       .setStart(10L)
       .setEnd(13L)
       .setSequence("AAA")
@@ -231,7 +231,7 @@ class RealignIndelsSuite extends ADAMFunSuite {
       .setReadMapped(true)
       .setMismatchingPositions("3")
       .build(), AlignmentRecord.newBuilder()
-      .setContig(ctg)
+      .setContigName(ctg.getContigName)
       .setStart(4L)
       .setEnd(7L)
       .setSequence("AAA")
@@ -240,7 +240,7 @@ class RealignIndelsSuite extends ADAMFunSuite {
       .setReadMapped(true)
       .setMismatchingPositions("3")
       .build(), AlignmentRecord.newBuilder()
-      .setContig(ctg)
+      .setContigName(ctg.getContigName)
       .setStart(7L)
       .setEnd(10L)
       .setSequence("AAA")
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rich/DecadentReadSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rich/DecadentReadSuite.scala
index 960672382c..5ae3155d12 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rich/DecadentReadSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rich/DecadentReadSuite.scala
@@ -36,7 +36,7 @@ class DecadentReadSuite extends ADAMFunSuite {
       .newBuilder()
       .setReadMapped(true)
       .setStart(1000)
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setMismatchingPositions("10")
       .setSequence("AACCTTGGC")
       .setQual("FFFFFFFFF")
@@ -58,7 +58,7 @@ class DecadentReadSuite extends ADAMFunSuite {
       .newBuilder()
       .setReadMapped(true)
       .setStart(1000)
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setMismatchingPositions("1TT10")
       .setSequence("ATTGGGGGGGGGG")
       .setQual("FFFFFFFFFFFFF")
@@ -80,7 +80,7 @@ class DecadentReadSuite extends ADAMFunSuite {
       .newBuilder()
       .setReadMapped(true)
       .setStart(1000)
-      .setContig(contig)
+      .setContigName(contig.getContigName)
       .setMismatchingPositions("10")
       .setSequence("AACCTTGGC")
       .setCigar("9M1H").build())
@@ -91,9 +91,7 @@ class DecadentReadSuite extends ADAMFunSuite {
 
   test("converting bad read should fail") {
     val readBad = AlignmentRecord.newBuilder()
-      .setContig(Contig.newBuilder()
-        .setContigName("1")
-        .build())
+      .setContigName("1")
       .setStart(248262648L)
       .setEnd(248262721L)
       .setMapq(23)
@@ -111,9 +109,7 @@ class DecadentReadSuite extends ADAMFunSuite {
 
   def badGoodReadRDD: RDD[AlignmentRecord] = {
     val readBad = AlignmentRecord.newBuilder()
-      .setContig(Contig.newBuilder()
-        .setContigName("1")
-        .build())
+      .setContigName("1")
       .setStart(248262648L)
       .setEnd(248262721L)
       .setMapq(23)
@@ -124,9 +120,7 @@ class DecadentReadSuite extends ADAMFunSuite {
       .setMismatchingPositions("3^C71")
       .build()
     val readGood = AlignmentRecord.newBuilder()
-      .setContig(Contig.newBuilder()
-        .setContigName("1")
-        .build())
+      .setContigName("1")
       .setStart(248262648L)
       .setEnd(248262721L)
       .setMapq(23)
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala
index 804f967fa9..ca90d2f6c8 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala
@@ -69,14 +69,14 @@ class RichAlignmentRecordSuite extends FunSuite {
 
   test("Cigar Clipping Sequence") {
     val contig = Contig.newBuilder.setContigName("chr1").build
-    val softClippedRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(100).setCigar("10S90M").setContig(contig).build()
+    val softClippedRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(100).setCigar("10S90M").setContigName(contig.getContigName).build()
     assert(softClippedRead.referencePositions(0).map(_.pos) == Some(90L))
 
   }
 
   test("tags contains optional fields") {
     val contig = Contig.newBuilder.setContigName("chr1").build
-    val rec = AlignmentRecord.newBuilder().setAttributes("XX:i:3\tYY:Z:foo").setContig(contig).build()
+    val rec = AlignmentRecord.newBuilder().setAttributes("XX:i:3\tYY:Z:foo").setContigName(contig.getContigName).build()
     assert(rec.tags.size === 2)
     assert(rec.tags(0) === Attribute("XX", TagType.Integer, 3))
     assert(rec.tags(1) === Attribute("YY", TagType.String, "foo"))
@@ -86,36 +86,36 @@ class RichAlignmentRecordSuite extends FunSuite {
 
     val contig = Contig.newBuilder.setContigName("chr1").build
 
-    val hardClippedRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("90M10H").setContig(contig).build()
+    val hardClippedRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("90M10H").setContigName(contig.getContigName).build()
     assert(hardClippedRead.referencePositions.length == 90)
     assert(hardClippedRead.referencePositions(0).map(_.pos) == Some(1000L))
 
-    val softClippedRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("10S90M").setContig(contig).build()
+    val softClippedRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("10S90M").setContigName(contig.getContigName).build()
     assert(softClippedRead.referencePositions.length == 100)
     assert(softClippedRead.referencePositions(0).map(_.pos) == Some(990L))
     assert(softClippedRead.referencePositions(10).map(_.pos) == Some(1000L))
 
-    val doubleMatchNonsenseRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("10M10M").setContig(contig).build()
+    val doubleMatchNonsenseRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("10M10M").setContigName(contig.getContigName).build()
     Range(0, 20).foreach(i => assert(doubleMatchNonsenseRead.referencePositions(i).map(_.pos) == Some(1000 + i)))
 
-    val deletionRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("5M5D10M").setContig(contig).build()
+    val deletionRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("5M5D10M").setContigName(contig.getContigName).build()
     assert(deletionRead.referencePositions.length == 15)
     assert(deletionRead.referencePositions(0).map(_.pos) == Some(1000L))
     assert(deletionRead.referencePositions(5).map(_.pos) == Some(1010L))
 
-    val insertionRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("10M2I10M").setContig(contig).build()
+    val insertionRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("10M2I10M").setContigName(contig.getContigName).build()
     assert(insertionRead.referencePositions.length == 22)
     assert(insertionRead.referencePositions(0).map(_.pos) == Some(1000L))
     assert(insertionRead.referencePositions(10).map(_.pos) == None)
     assert(insertionRead.referencePositions(12).map(_.pos) == Some(1010L))
 
-    val indelRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("10M3D10M2I").setContig(contig).build()
+    val indelRead = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("10M3D10M2I").setContigName(contig.getContigName).build()
     assert(indelRead.referencePositions.length == 22)
     assert(indelRead.referencePositions(0).map(_.pos) == Some(1000L))
     assert(indelRead.referencePositions(10).map(_.pos) == Some(1013L))
     assert(indelRead.referencePositions(20).map(_.pos) == None)
 
-    val hg00096read = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("1S28M1D32M1I15M1D23M").setContig(contig).build()
+    val hg00096read = AlignmentRecord.newBuilder().setReadMapped(true).setStart(1000).setCigar("1S28M1D32M1I15M1D23M").setContigName(contig.getContigName).build()
     assert(hg00096read.referencePositions.length == 100)
     assert(hg00096read.referencePositions(0).map(_.pos) == Some(999L))
     assert(hg00096read.referencePositions(1).map(_.pos) == Some(1000L))
@@ -137,7 +137,7 @@ class RichAlignmentRecordSuite extends FunSuite {
   test("read overlap reference position") {
 
     val contig = Contig.newBuilder.setContigName("chr1").build
-    val record = RichAlignmentRecord(AlignmentRecord.newBuilder().setReadMapped(true).setCigar("10M").setStart(10L).setEnd(20L).setContig(contig).build())
+    val record = RichAlignmentRecord(AlignmentRecord.newBuilder().setReadMapped(true).setCigar("10M").setStart(10L).setEnd(20L).setContigName(contig.getContigName).build())
 
     assert(record.overlapsReferencePosition(ReferencePosition("chr1", 10)) == true)
     assert(record.overlapsReferencePosition(ReferencePosition("chr1", 14)) == true)
@@ -148,7 +148,7 @@ class RichAlignmentRecordSuite extends FunSuite {
   test("read overlap same position different contig") {
 
     val contig = Contig.newBuilder.setContigName("chr1").build
-    val record = RichAlignmentRecord(AlignmentRecord.newBuilder().setReadMapped(true).setCigar("10M").setStart(10L).setEnd(20L).setContig(contig).build())
+    val record = RichAlignmentRecord(AlignmentRecord.newBuilder().setReadMapped(true).setCigar("10M").setStart(10L).setEnd(20L).setContigName(contig.getContigName).build())
 
     assert(record.overlapsReferencePosition(ReferencePosition("chr2", 10)) == false)
   }
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/util/UtilSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/util/UtilSuite.scala
index 0d4069d784..c222e1d8aa 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/util/UtilSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/util/UtilSuite.scala
@@ -24,20 +24,23 @@ class UtilSuite extends ADAMFunSuite {
   test("isSameConfig") {
     val a = Contig.newBuilder().setContigName("foo")
     val b = Contig.newBuilder().setContigName("bar")
-    assert(!Util.isSameContig(a.build(), b.build()))
+    assert(!Util.isSameContig(a.build().getContigName, b.build().getContigName))
     b.setContigName("foo")
-    assert(Util.isSameContig(a.build(), b.build()))
+    assert(Util.isSameContig(a.build().getContigName, b.build().getContigName))
 
     // proper null handling
     assert(Util.isSameContig(null, null))
-    assert(!Util.isSameContig(null, b.build()))
-    assert(!Util.isSameContig(a.build(), null))
+    assert(!Util.isSameContig(null, b.build().getContigName))
+    assert(!Util.isSameContig(a.build().getContigName, null))
 
-    a.setContigMD5("md5")
+    // Prior to removing Contig from AlignmentRecprd the code below
+    // tested for MD5 concordance.  We may want to revisit how contig MD5 concordance
+    // is checked in future
+    //a.setContigMD5("md5")
     // both md5s need to be set to change equality
-    assert(!Util.isSameContig(a.build(), b.build()))
-    b.setContigMD5("md5")
-    assert(Util.isSameContig(a.build(), b.build()))
+    //assert(!Util.isSameContig(a.build().getContigName, b.build().getContigName))
+    //b.setContigMD5("md5")
+    //assert(Util.isSameContig(a.build().getContigName, b.build().getContigName))
   }
 
 }
diff --git a/pom.xml b/pom.xml
index 274496a2ba..752b652656 100644
--- a/pom.xml
+++ b/pom.xml
@@ -316,7 +316,7 @@
       <dependency>
         <groupId>org.bdgenomics.bdg-formats</groupId>
         <artifactId>bdg-formats</artifactId>
-        <version>0.7.0</version>
+        <version>0.7.2-SNAPSHOT</version>
       </dependency>
       <dependency>
         <groupId>commons-io</groupId>