From e9183d9fe0ada286ed91bced4feb1e004e10ad56 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 8 Nov 2012 15:07:47 -0500
Subject: [PATCH] Fix bugs as reported on the forum: BED needs to be explicitly
 set as the default output format and the output didn't actually adhere to the
 BED spec.

---
 .../sting/gatk/walkers/coverage/CallableLoci.java         | 4 ++--
 .../coverage/CallableLociWalkerIntegrationTest.java       | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
index 58ddd0879..48019efea 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
@@ -191,7 +191,7 @@ public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, Ca
      */
     @Advanced
     @Argument(fullName = "format", shortName = "format", doc = "Output format", required = false)
-    OutputFormat outputFormat;
+    OutputFormat outputFormat = OutputFormat.BED;
 
     public enum OutputFormat {
         /**
@@ -297,7 +297,7 @@ public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, Ca
         }
 
         public String toString() {
-            return String.format("%s %d %d %s", loc.getContig(), loc.getStart(), loc.getStop(), state);
+            return String.format("%s\t%d\t%d\t%s", loc.getContig(), loc.getStart()-1, loc.getStop(), state);
         }
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
index c9e91e664..ec69a893c 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociWalkerIntegrationTest.java
@@ -38,7 +38,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
     public void testCallableLociWalkerBed() {
         String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -summary %s";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
-                Arrays.asList("9e4ec9c23f21a8162d27a39ab057398c", SUMMARY_MD5));
+                Arrays.asList("42e86c06c167246a28bffdacaca75ffb", SUMMARY_MD5));
         executeTest("formatBed", spec);
     }
 
@@ -46,7 +46,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
     public void testCallableLociWalkerPerBase() {
         String gatk_args = commonArgs + " -format STATE_PER_BASE -L 1:10,000,000-11,000,000 -summary %s";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
-                Arrays.asList("e6044b4495ef24f542403e6a94437068", SUMMARY_MD5));
+                Arrays.asList("d66c525d9c70f62df8156261d3e535ad", SUMMARY_MD5));
         executeTest("format_state_per_base", spec);
     }
     
@@ -54,7 +54,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
     public void testCallableLociWalker2() {
         String gatk_args = commonArgs + " -format BED -L 1:10,000,000-10,000,100 -L 1:10,000,110-10,000,120 -summary %s";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
-                Arrays.asList("c671f65712d9575b8b3e1f1dbedc146e", "d287510eac04acf5a56f5cde2cba0e4a"));
+                Arrays.asList("330f476085533db92a9dbdb3a127c041", "d287510eac04acf5a56f5cde2cba0e4a"));
         executeTest("formatBed by interval", spec);
     }
 
@@ -62,7 +62,7 @@ public class CallableLociWalkerIntegrationTest extends WalkerTest {
     public void testCallableLociWalker3() {
         String gatk_args = commonArgs + " -format BED -L 1:10,000,000-11,000,000 -minDepth 10 -maxDepth 100 --minBaseQuality 10 --minMappingQuality 20 -summary %s";
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 2,
-                Arrays.asList("b7d26a470ef906590249f2fa45fd6bdd", "da431d393f7c2b2b3e27556b86c1dbc7"));
+                Arrays.asList("46a53379aaaf9803276a0a34b234f6ab", "da431d393f7c2b2b3e27556b86c1dbc7"));
         executeTest("formatBed lots of arguments", spec);
     }
 }