From 77f2374cecf52aeaea309eda148bef13ecce0872 Mon Sep 17 00:00:00 2001
From: Hao Hou <haohou302@gmail.com>
Date: Thu, 7 Nov 2019 12:17:57 -0700
Subject: [PATCH] Fix issue #788 and add test cases

---
 src/utils/BamTools/include/BamAlignment.hpp |  6 ++---
 test/bedtobam/chrsize.tmp                   |  1 +
 test/bedtobam/test-bedtobam.sh              | 26 +++++++++++++++++++++
 3 files changed, 30 insertions(+), 3 deletions(-)
 create mode 100644 test/bedtobam/chrsize.tmp
 create mode 100644 test/bedtobam/test-bedtobam.sh

diff --git a/src/utils/BamTools/include/BamAlignment.hpp b/src/utils/BamTools/include/BamAlignment.hpp
index 96e8ebbef..c25cd008f 100644
--- a/src/utils/BamTools/include/BamAlignment.hpp
+++ b/src/utils/BamTools/include/BamAlignment.hpp
@@ -187,10 +187,10 @@ namespace BamTools {
 		bool SyncExtraData() const
 		{
 #define BAM_DATA_OFFSET(what) ((size_t)(((uint8_t*)bam_get_##what(&_bam)) - ((uint8_t*)_bam.data)))
-			void* qname_buf = _ensure_data_chunk((bam1_t*)&_bam, BAM_DATA_OFFSET(qname), _bam.core.l_qname, Name.size());
+			void* qname_buf = _ensure_data_chunk((bam1_t*)&_bam, BAM_DATA_OFFSET(qname), _bam.core.l_qname, Name.size() + 1);
 			if(NULL == qname_buf) return false;
-			memcpy(qname_buf, Name.c_str(), Name.size());
-			((bam1_t*)&_bam)->core.l_qname = Name.size();
+			memcpy(qname_buf, Name.c_str(), Name.size() + 1);
+			((bam1_t*)&_bam)->core.l_qname = Name.size() + 1;
 
 			uint32_t* cigar_buf = (uint32_t*)_ensure_data_chunk((bam1_t*)&_bam, BAM_DATA_OFFSET(cigar), _bam.core.n_cigar * sizeof(uint32_t), sizeof(uint32_t) * CigarData.size());
 			if(NULL == cigar_buf) return false;
diff --git a/test/bedtobam/chrsize.tmp b/test/bedtobam/chrsize.tmp
new file mode 100644
index 000000000..d2e5cdd95
--- /dev/null
+++ b/test/bedtobam/chrsize.tmp
@@ -0,0 +1 @@
+1	3000
diff --git a/test/bedtobam/test-bedtobam.sh b/test/bedtobam/test-bedtobam.sh
new file mode 100644
index 000000000..1003ff307
--- /dev/null
+++ b/test/bedtobam/test-bedtobam.sh
@@ -0,0 +1,26 @@
+set -e;
+BT=${BT-../../bin/bedtools}
+
+FAILURES=0;
+
+check()
+{
+	if diff $1 $2; then
+    	echo ok
+	else
+		FAILURES=$(expr $FAILURES + 1);
+		echo fail
+	fi
+}
+
+##################################################################
+#  Test one block without -split
+##################################################################
+echo -e "    bedtobam.t1...\c"
+echo \
+"read_name	0	1	1001	255	1000M	*	0	0	*	*">exp
+echo -e "1\t1000\t2000\tread_name\t255\t+" | $BT bedtobam -i - -g chrsize.tmp| samtools view > obs
+check obs exp
+rm obs exp
+
+[[ $FAILURES -eq 0 ]] || exit 1;