public RecordWriter<K,SAMRecordWritable> getRecordWriter( TaskAttemptContext ctx, Path out) throws IOException { if (this.header == null) throw new IOException( "Can't create a RecordWriter without the SAM header"); return new KeyIgnoringCRAMRecordWriter<K>(out, header, writeHeader, ctx); } }
public RecordWriter<K,SAMRecordWritable> getRecordWriter( TaskAttemptContext ctx, Path out) throws IOException { if (this.header == null) throw new IOException( "Can't create a RecordWriter without the SAM header"); return new KeyIgnoringCRAMRecordWriter<K>(out, header, writeHeader, ctx); } }
public RecordWriter<K,SAMRecordWritable> getRecordWriter( TaskAttemptContext ctx, Path out) throws IOException { if (this.header == null) throw new IOException( "Can't create a RecordWriter without the SAM header"); return new KeyIgnoringCRAMRecordWriter<K>(out, header, writeHeader, ctx); } }
public RecordWriter<K,SAMRecordWritable> getRecordWriter( TaskAttemptContext ctx, Path out) throws IOException { if (this.header == null) throw new IOException( "Can't create a RecordWriter without the SAM header"); final boolean writeHeader = ctx.getConfiguration().getBoolean( WRITE_HEADER_PROPERTY, writeHeader_); switch (format) { case BAM: return new KeyIgnoringBAMRecordWriter<K>( out, header, writeHeader, ctx); case SAM: return new KeyIgnoringSAMRecordWriter<K>( out, header, writeHeader, ctx); case CRAM: return new KeyIgnoringCRAMRecordWriter<K>( out, header, writeHeader, ctx); default: assert false; return null; } } }
public RecordWriter<K,SAMRecordWritable> getRecordWriter( TaskAttemptContext ctx, Path out) throws IOException { if (this.header == null) throw new IOException( "Can't create a RecordWriter without the SAM header"); final boolean writeHeader = ctx.getConfiguration().getBoolean( WRITE_HEADER_PROPERTY, writeHeader_); switch (format) { case BAM: return new KeyIgnoringBAMRecordWriter<K>( out, header, writeHeader, ctx); case SAM: return new KeyIgnoringSAMRecordWriter<K>( out, header, writeHeader, ctx); case CRAM: return new KeyIgnoringCRAMRecordWriter<K>( out, header, writeHeader, ctx); default: assert false; return null; } } }
public RecordWriter<K,SAMRecordWritable> getRecordWriter( TaskAttemptContext ctx, Path out) throws IOException { if (this.header == null) throw new IOException( "Can't create a RecordWriter without the SAM header"); final boolean writeHeader = ctx.getConfiguration().getBoolean( WRITE_HEADER_PROPERTY, true); switch (format) { case BAM: return new KeyIgnoringBAMRecordWriter<K>( out, header, writeHeader, ctx); case SAM: return new KeyIgnoringSAMRecordWriter<K>( out, header, writeHeader, ctx); case CRAM: return new KeyIgnoringCRAMRecordWriter<K>( out, header, writeHeader, ctx); default: assert false; return null; } } }