fix for changes

heuermh · heuermh · commit a895649d542e · 2021-02-23T11:57:52.000-06:00
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
@@ -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
@@ -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()

Original file line number	Diff line number	Diff line change
`@@ -224,7 +224,7 @@ private[adam] object FileMerger extends Logging {`
`224`	`224`	`if (writeEmptyGzipBlock) {`
`225`	`225`	`os.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK)`
`226`	`226`	`} else if (writeCramEOF) {`
`227`		`- CramIO.issueEOF(CramVersions.DEFAULT_CRAM_VERSION, os)`
	`227`	`+ CramIO.writeCramEOF(CramVersions.DEFAULT_CRAM_VERSION, os)`
`228`	`228`	`}`
`229`	`229`
`230`	`230`	`// flush and close the output stream`
Original file line number	Diff line number	Diff line change
`@@ -97,7 +97,7 @@ private[adam] object ParallelFileMerger extends Logging {`
`97`	`97`	`if (writeEmptyGzipBlock) {`
`98`	`98`	`os.write(BlockCompressedStreamConstants.EMPTY_GZIP_BLOCK)`
`99`	`99`	`} else if (writeCramEOF) {`
`100`		`- CramIO.issueEOF(CramVersions.DEFAULT_CRAM_VERSION, os)`
	`100`	`+ CramIO.writeCramEOF(CramVersions.DEFAULT_CRAM_VERSION, os)`
`101`	`101`	`}`
`102`	`102`
`103`	`103`	`os.flush()`