diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java index cb8786be1..300e801e6 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java +++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java @@ -62,6 +62,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage { @Output(required=false, doc="Output bam") protected StingSAMFileWriter writer = null; - /** - * If set too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool - * may run out of memory. We recommend that you additionally tell Java to use a temp directory with plenty of available - * space (by setting java.io.tempdir on the command-line). - */ - @Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the output writer", required=false) - protected int MAX_RECORDS_IN_RAM = 500000; - - public void initialize() { - // set up the output writer - if ( writer != null ) - writer.setMaxRecordsInRam(MAX_RECORDS_IN_RAM); - } + public void initialize() {} private void emit(final SAMRecord read) { if ( writer != null )