From 8f19dab39e5a9b9f0e4e31b49a66fd6085704de7 Mon Sep 17 00:00:00 2001 From: Frank Austin Nothaft Date: Fri, 15 Dec 2017 15:33:39 -0800 Subject: [PATCH] Specifies correct extensions for various file formats. Resolves #175. --- src/main/java/org/seqdoop/hadoop_bam/FastqOutputFormat.java | 2 +- .../org/seqdoop/hadoop_bam/KeyIgnoringAnySAMOutputFormat.java | 2 +- .../java/org/seqdoop/hadoop_bam/KeyIgnoringBAMOutputFormat.java | 2 +- .../org/seqdoop/hadoop_bam/KeyIgnoringCRAMOutputFormat.java | 2 +- .../java/org/seqdoop/hadoop_bam/KeyIgnoringVCFOutputFormat.java | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/main/java/org/seqdoop/hadoop_bam/FastqOutputFormat.java b/src/main/java/org/seqdoop/hadoop_bam/FastqOutputFormat.java index 3550c89..07fefa1 100644 --- 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 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 index 64de49d..e60fbe5 100644 --- 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 index 4670214..bd27837 100644 --- 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 index c7a4126..69b8379 100644 --- 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 index 04282c8..a58c86f 100644 --- 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 codecClass = getOutputCompressorClass(ctx, BGZFCodec.class);