From 0b4281fdd081798481267c69b9b0c473bb8d0253 Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Thu, 7 Jun 2012 10:56:41 -0400
Subject: [PATCH] misc minor update to HC debug output for when there are a lot
 of samples

---
 .../org/broadinstitute/sting/utils/sam/ReadUtils.java    | 1 -
 .../sting/utils/variantcontext/VariantContext.java       | 9 +++++++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 4e2fd1446..820a9b731 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -553,7 +553,6 @@ public class ReadUtils {
         return true;
     }
 
-
     /**
      * Checks if a read starts with an insertion. It looks beyond Hard and Soft clips
      * if there are any.
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index cb31fe308..bb06357ad 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1264,6 +1264,15 @@ public class VariantContext implements Feature { // to enable tribble integratio
                 this.getGenotypes());
     }
 
+    public String toStringWithoutGenotypes() {
+        return String.format("[VC %s @ %s Q%s of type=%s alleles=%s attr=%s",
+                getSource(), contig + ":" + (start - stop == 0 ? start : start + "-" + stop),
+                hasLog10PError() ? String.format("%.2f", getPhredScaledQual()) : ".",
+                this.getType(),
+                ParsingUtils.sortList(this.getAlleles()),
+                ParsingUtils.sortedString(this.getAttributes()));
+    }
+
     // protected basic manipulation routines
     private static List<Allele> makeAlleles(Collection<Allele> alleles) {
         final List<Allele> alleleList = new ArrayList<Allele>(alleles.size());