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Specifies correct extensions for various file formats #176

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Specifies correct extensions for various file formats #176

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2 changes: 1 addition & 1 deletion src/main/java/org/seqdoop/hadoop_bam/FastqOutputFormat.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
{
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2 changes: 1 addition & 1 deletion src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringAnySAMOutputFormat.java
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringBAMOutputFormat.java
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringCRAMOutputFormat.java
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion src/main/java/org/seqdoop/hadoop_bam/KeyIgnoringVCFOutputFormat.java
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Expand Up @@ -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";
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Won't this get replaced by the compressor extension in the next code block anyway? So it will be "file.bgz" not "file.vcf.bgz".

if (isCompressed) {
Class<? extends CompressionCodec> codecClass =
getOutputCompressorClass(ctx, BGZFCodec.class);
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