diff --git a/Makefile b/Makefile
index b5e85913e21af79124dc51cb719e717e17fea7e5..9f4ba8e6a2a50e17921fb564b2e1f8b1d9173ee2 100644
--- a/Makefile
+++ b/Makefile
@@ -18,7 +18,7 @@ TOOLS=-DSAMTOOLS=\"$(SAMTOOLS)\" -DBWA=\"$(BWA)\" -DSICKLE=\"$(SICKLE)\" -DVELVE
 
 # Date and version number from git
 DATE := on $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1)
-VERSION := 0.0.4-snake-$(shell git log --pretty=format:"%h" --date=iso | head -n 1)
+VERSION := 0.0.5-snake-$(shell git log --pretty=format:"%h" --date=iso | head -n 1)
 CXXFLAGS += -DDATE=\""$(DATE)"\" -DVERSION=\""$(VERSION)"\"
 
 # Compiler flags
diff --git a/src/popins2_merge_and_set_mate.h b/src/popins2_merge_and_set_mate.h
index 588e8c41751a37943e3fe9101729c0d8d90a1aff..7205ff28dcd2fb151ed33283c67a5048e5ad6bd2 100644
--- a/src/popins2_merge_and_set_mate.h
+++ b/src/popins2_merge_and_set_mate.h
@@ -101,6 +101,7 @@ inline void readRecordAndCorrectRIds(BamAlignmentRecord & record, BamFileIn & st
 // ==========================================================================
 
 inline void mergeHeaders(BamHeader & header, FormattedFileContext<BamFileOut, Owner<> >::Type & context, BamFileIn & stream1, BamFileIn & stream2){
+
     StringSet<CharString> contigNames;
     NameStoreCache<StringSet<CharString> > nameStoreCache;
     String<int32_t> contigLengths;
@@ -109,11 +110,35 @@ inline void mergeHeaders(BamHeader & header, FormattedFileContext<BamFileOut, Ow
     readHeader(header, stream1);
     BamHeader header2;
     readHeader(header2, stream2);
-    for (unsigned i = 0; i < length(header2); ++i)
-    {
-        if (header2[i].type != BAM_HEADER_FIRST)
+
+    std::unordered_set<char*> program_ids;
+
+    for (unsigned i = 0; i < length(header2); ++i){
+
+        if (header2[i].type != BAM_HEADER_FIRST){
+
+            if (header2[i].type == BAM_HEADER_PROGRAM){
+                CharString PG_ID;
+                bool keyFound = getTagValue(PG_ID, "ID", header2[i]);
+
+                if ( program_ids.find(toCString(PG_ID)) != program_ids.end() ){     // if PG ID was seen already
+                    BamHeaderRecord hrecord = header2[i];
+                    CharString suf = ".mH";                                         // mH = "mergeHeader" to trace in SAM/BAM files
+                    append(PG_ID, suf);
+                    setTagValue("ID", PG_ID, hrecord);
+                    appendValue(header, hrecord);
+                    continue;
+                }
+                else{
+                    program_ids.insert(toCString(PG_ID));
+                }
+
+            }
+
             appendValue(header, header2[i]);
+        }
     }
+
     std::stable_sort(begin(header, Standard()), end(header, Standard()), BamHeaderRecordTypeLess());
 
     // Fill sequence names into nameStoreCache.