diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java index 59118f8b0..769e4dc30 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java @@ -92,12 +92,7 @@ public class GLFWriter implements GenotypeWriter { int readDepth, LikelihoodObject lhValues) { - getRidOfMe++; - if (getRidOfMe == 500) { - this.close(); - } else if (getRidOfMe < 500) { - System.err.println(contig.getSequenceName() + ":" + genomicLoc); - // check if we've jumped to a new contig + // check if we've jumped to a new contig checkSequence(contig.getSequenceName(), contig.getSequenceLength()); SinglePointCall call = new SinglePointCall(refBase, @@ -107,7 +102,6 @@ public class GLFWriter implements GenotypeWriter { lhValues.toDoubleArray()); lastPos = genomicLoc; call.write(this.outputBinaryCodec); - } } /**