Specifies correct extensions for various file formats. Resolves Hadoo…

…pGenomics#175.
fnothaft · Dec 15, 2017 · 8f19dab · 8f19dab
1 parent 0c54715
commit 8f19dab
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Showing 5 changed files with 5 additions and 5 deletions.
diff --git a/src/main/java/org/seqdoop/hadoop_bam/FastqOutputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/FastqOutputFormat.java
@@ -157,7 +157,7 @@ public RecordWriter<Text,SequencedFragment> getRecordWriter(TaskAttemptContext t
 		boolean isCompressed = getCompressOutput(task);
 
 		CompressionCodec codec = null;
-		String extension = "";
+		String extension = ".fastq";
 
 		if (isCompressed)
 		{

diff --git a/src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringAnySAMOutputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringAnySAMOutputFormat.java
@@ -108,7 +108,7 @@ public void readSAMHeaderFrom(InputStream in, Configuration conf) {
 			TaskAttemptContext ctx)
 		throws IOException
 	{
-		return getRecordWriter(ctx, getDefaultWorkFile(ctx, ""));
+		return getRecordWriter(ctx, getDefaultWorkFile(ctx, ".sam"));
 	}
 
 	// Allows wrappers to provide their own work file.

diff --git a/src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringBAMOutputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringBAMOutputFormat.java
@@ -76,7 +76,7 @@ public void readSAMHeaderFrom(InputStream in, Configuration conf) {
 			TaskAttemptContext ctx)
 		throws IOException
 	{
-		return getRecordWriter(ctx, getDefaultWorkFile(ctx, ""));
+		return getRecordWriter(ctx, getDefaultWorkFile(ctx, ".bam"));
 	}
 
 	// Allows wrappers to provide their own work file.

diff --git a/src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringCRAMOutputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringCRAMOutputFormat.java
@@ -54,7 +54,7 @@ public void readSAMHeaderFrom(InputStream in, Configuration conf) {
             TaskAttemptContext ctx)
             throws IOException
     {
-        return getRecordWriter(ctx, getDefaultWorkFile(ctx, ""));
+        return getRecordWriter(ctx, getDefaultWorkFile(ctx, ".cram"));
     }
 
     // Allows wrappers to provide their own work file.

diff --git a/src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringVCFOutputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringVCFOutputFormat.java
@@ -97,7 +97,7 @@ public void readHeaderFrom(SeekableStream in) throws IOException {
 		Configuration conf = ctx.getConfiguration();
 		boolean isCompressed = getCompressOutput(ctx);
 		CompressionCodec codec = null;
-		String extension = "";
+		String extension = ".vcf";
 		if (isCompressed) {
 			Class<? extends CompressionCodec> codecClass =
 					getOutputCompressorClass(ctx, BGZFCodec.class);