From 18950f7a0a56d5703694ea5962a3b8f38668bbc5 Mon Sep 17 00:00:00 2001
From: Michael L Heuer <heuermh@acm.org>
Date: Sat, 10 Aug 2019 12:03:26 -0500
Subject: [PATCH] Update htsjdk dependency version to 2.24.1.

---
 .../src/main/scala/org/bdgenomics/adam/util/FileMerger.scala  | 2 +-
 .../scala/org/bdgenomics/adam/util/ParallelFileMerger.scala   | 2 +-
 pom.xml                                                       | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/util/FileMerger.scala b/adam-core/src/main/scala/org/bdgenomics/adam/util/FileMerger.scala
index c08e7ecca5..3c6fe129da 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/util/FileMerger.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/util/FileMerger.scala
@@ -224,7 +224,7 @@ private[adam] object FileMerger extends Logging {
     if (writeEmptyGzipBlock) {
       os.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK)
     } else if (writeCramEOF) {
-      CramIO.issueEOF(CramVersions.DEFAULT_CRAM_VERSION, os)
+      CramIO.writeCramEOF(CramVersions.DEFAULT_CRAM_VERSION, os)
     }
 
     // flush and close the output stream
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/util/ParallelFileMerger.scala b/adam-core/src/main/scala/org/bdgenomics/adam/util/ParallelFileMerger.scala
index 403ea9ec44..9f13362f0f 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/util/ParallelFileMerger.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/util/ParallelFileMerger.scala
@@ -97,7 +97,7 @@ private[adam] object ParallelFileMerger extends Logging {
     if (writeEmptyGzipBlock) {
       os.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK)
     } else if (writeCramEOF) {
-      CramIO.issueEOF(CramVersions.DEFAULT_CRAM_VERSION, os)
+      CramIO.writeCramEOF(CramVersions.DEFAULT_CRAM_VERSION, os)
     }
 
     os.flush()
diff --git a/pom.xml b/pom.xml
index d7e8732ff3..9119170d6d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -23,12 +23,12 @@
     <scala.version.prefix>2.12</scala.version.prefix>
     <spark.version>3.2.0</spark.version>
     <parquet.version>1.12.1</parquet.version>
-    <hadoop-bam.version>7.9.2</hadoop-bam.version>
+    <hadoop-bam.version>7.10.0</hadoop-bam.version>
     <slf4j.version>1.7.30</slf4j.version>
     <bdg-formats.version>0.17.0-SNAPSHOT</bdg-formats.version>
     <bdg-utils.version>0.4.0</bdg-utils.version>
     <grizzled-slf4j.version>1.3.4</grizzled-slf4j.version>
-    <htsjdk.version>2.19.0</htsjdk.version>
+    <htsjdk.version>2.24.1</htsjdk.version>
     <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
   </properties>