From d2c19bda20910a35c8430d55bf0ebf82a2f1ff3e Mon Sep 17 00:00:00 2001
From: hxdhan <hxdhan@qq.com>
Date: Wed, 23 Jun 2021 11:21:48 +0800
Subject: [PATCH] add SAMFileHeader

---
 .../bdgenomics/adam/ds/read/AnySAMOutFormatter.scala | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMOutFormatter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMOutFormatter.scala
index bf61a88f4a..f55b54a678 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMOutFormatter.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMOutFormatter.scala
@@ -24,14 +24,16 @@ import org.bdgenomics.adam.ds.OutFormatter
 import org.bdgenomics.formats.avro.Alignment
 import scala.annotation.tailrec
 import scala.collection.mutable.ListBuffer
+import java.io.{ BufferedReader, InputStreamReader }
+import org.bdgenomics.adam.ds._
 
 /**
  * An OutFormatter that automatically infers whether the piped input is SAM or
  * BAM. Autodetecting streamed CRAM is not currently supported.
  */
-case class AnySAMOutFormatter(stringency: ValidationStringency) extends OutFormatter[Alignment] {
+case class AnySAMOutFormatter(stringency: ValidationStringency, header: SAMFileHeader) extends OutFormatter[Alignment] {
 
-  def this() = this(ValidationStringency.STRICT)
+  def this() = this(ValidationStringency.STRICT, new SAMFileHeader())
 
   /**
    * Reads alignments from an input stream. Autodetects SAM/BAM format.
@@ -46,6 +48,12 @@ case class AnySAMOutFormatter(stringency: ValidationStringency) extends OutForma
       .validationStringency(stringency)
       .open(SamInputResource.of(is))
 
+    //copy reader header
+    val r_header = reader.getFileHeader()
+    header.setSequenceDictionary(r_header.getSequenceDictionary())
+    header.setReadGroups(r_header.getReadGroups())
+    header.setProgramRecords(r_header.getProgramRecords())
+
     SAMIteratorConverter(reader)
   }
 }