diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.scala
index 44a4deeb17..5a74aa3928 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.scala
@@ -80,8 +80,18 @@ class InterleavedFASTQInFormatter private (
         outputOriginalBaseQualities = writeOriginalQualities) + "\n"
 
       // write both to the output stream
-      os.write(fastq1.getBytes)
-      os.write(fastq2.getBytes)
+      // ensure that reads are ordered properly if ordering is known (see #1702)
+      if (read1.getReadInFragment == 0 &&
+        read2.getReadInFragment == 1) {
+        os.write(fastq1.getBytes)
+        os.write(fastq2.getBytes)
+      } else if (read1.getReadInFragment == 1 &&
+        read2.getReadInFragment == 0) {
+        os.write(fastq2.getBytes)
+        os.write(fastq1.getBytes)
+      } else {
+        log.warn("Improper pair of reads in fragment %s. Dropping...".format(p))
+      }
     })
   }
 }
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.scala
index 09b308a4d0..754d622569 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.scala
@@ -29,7 +29,9 @@ import scala.collection.mutable.ListBuffer
  * An OutFormatter that automatically infers whether the piped input is SAM or
  * BAM. Autodetecting streamed CRAM is not currently supported.
  */
-class AnySAMOutFormatter extends OutFormatter[AlignmentRecord] {
+case class AnySAMOutFormatter(stringency: ValidationStringency) extends OutFormatter[AlignmentRecord] {
+
+  def this() = this(ValidationStringency.STRICT)
 
   /**
    * Reads alignment records from an input stream. Autodetects SAM/BAM format.
@@ -41,6 +43,7 @@ class AnySAMOutFormatter extends OutFormatter[AlignmentRecord] {
 
     // make reader
     val reader = SamReaderFactory.makeDefault()
+      .validationStringency(stringency)
       .open(SamInputResource.of(is))
 
     SAMIteratorConverter(reader)