From 3b09d42ed6d915c68c26df83f589edb4c83b70e5 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 29 Aug 2011 14:41:29 -0400
Subject: [PATCH] Now only prints 1 warning message about duplicate headers in
 simpleMerge

---
 .../sting/utils/codecs/vcf/VCFUtils.java      | 28 +++++++++++++++----
 1 file changed, 22 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
index c0a04c81f..2d8421507 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
@@ -116,10 +116,26 @@ public class VCFUtils {
         return fields;
     }
 
-    
+    /** Only displays a warning if a logger is provided and an identical warning hasn't been already issued */
+    private static final class HeaderConflictWarner {
+        Logger logger;
+        Set<String> alreadyIssued = new HashSet<String>();
+
+        private HeaderConflictWarner(final Logger logger) {
+            this.logger = logger;
+        }
+
+        public void warn(final VCFHeaderLine line, final String msg) {
+            if ( logger != null && ! alreadyIssued.contains(line.getKey()) ) {
+                alreadyIssued.add(line.getKey());
+                logger.warn(msg);
+            }
+        }
+    }
 
     public static Set<VCFHeaderLine> smartMergeHeaders(Collection<VCFHeader> headers, Logger logger) throws IllegalStateException {
         HashMap<String, VCFHeaderLine> map = new HashMap<String, VCFHeaderLine>(); // from KEY.NAME -> line
+        HeaderConflictWarner conflictWarner = new HeaderConflictWarner(logger);
 
         // todo -- needs to remove all version headers from sources and add its own VCF version line
         for ( VCFHeader source : headers ) {
@@ -152,24 +168,24 @@ public class VCFUtils {
                                 // number, then this value should be 1. However, if the INFO field describes a pair
                                 // of numbers, then this value should be 2 and so on. If the number of possible
                                 // values varies, is unknown, or is unbounded, then this value should be '.'.
-                                if ( logger != null ) logger.warn("Promoting header field Number to . due to number differences in header lines: " + line + " " + other);
+                                conflictWarner.warn(line, "Promoting header field Number to . due to number differences in header lines: " + line + " " + other);
                                 compOther.setNumberToUnbounded();
                             } else if ( compLine.getType() == VCFHeaderLineType.Integer && compOther.getType() == VCFHeaderLineType.Float ) {
                                 // promote key to Float
-                                if ( logger != null ) logger.warn("Promoting Integer to Float in header: " + compOther);
+                                conflictWarner.warn(line, "Promoting Integer to Float in header: " + compOther);
                                 map.put(key, compOther);
                             } else if ( compLine.getType() == VCFHeaderLineType.Float && compOther.getType() == VCFHeaderLineType.Integer ) {
                                 // promote key to Float
-                                if ( logger != null ) logger.warn("Promoting Integer to Float in header: " + compOther);
+                                conflictWarner.warn(line, "Promoting Integer to Float in header: " + compOther);
                             } else {
                                 throw new IllegalStateException("Incompatible header types, collision between these two types: " + line + " " + other );
                             }
                         }
                         if ( ! compLine.getDescription().equals(compOther) )
-                            if ( logger != null ) logger.warn("Allowing unequal description fields through: keeping " + compOther + " excluding " + compLine);
+                            conflictWarner.warn(line, "Allowing unequal description fields through: keeping " + compOther + " excluding " + compLine);
                     } else {
                         // we are not equal, but we're not anything special either
-                        if ( logger != null ) logger.warn("Ignoring header line already in map: this header line = " + line + " already present header = " + other);
+                        conflictWarner.warn(line, "Ignoring header line already in map: this header line = " + line + " already present header = " + other);
                     }
                 } else {
                     map.put(key, line);