Fix issue arq5x#803 and add test cases

38 · Dec 12, 2019 · 940ee18 · 940ee18
1 parent 77f2374
commit 940ee18
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Showing 2 changed files with 15 additions and 2 deletions.
diff --git a/src/utils/BamTools/include/SamHeader.hpp b/src/utils/BamTools/include/SamHeader.hpp
@@ -33,7 +33,7 @@ namespace htslib_future {
 
 		hts_close(fp);
 
-		hdr->l_text = buffer->length();
+		hdr->l_text = (uint32_t)buffer->length();
 		hdr->text = strdup(buffer->c_str());
 		delete buffer;
 
@@ -104,8 +104,9 @@ namespace BamTools {
 
 		void ParseHeaderText(const std::string& text)
 		{
-			_header = sam_hdr_parse(text.length(), text.c_str());
+			_header = sam_hdr_parse((int)text.length(), text.c_str());
 			_header->text = strdup(text.c_str());
+			_header->l_text = (uint32_t)text.length();
 		}
 		void destory() 
 		{

diff --git a/test/intersect/new_test-intersect.sh b/test/intersect/new_test-intersect.sh
@@ -968,3 +968,15 @@ $BT intersect -iobuf 2G -ubam -S -u -sorted -b a.bam -a a.bed >obs
 check exp obs
 rm exp obs
 [[ $FAILURES -eq 0 ]] || exit 1;
+
+
+
+###########################################################
+#  Test intersect preserve the text header in bam
+############################################################
+echo -e "    intersect.new.t78...\c"
+echo -e "@HD     VN:1.5  SO:coordinate" > exp
+echo "@HD     VN:1.5  SO:coordinate" | samtools view -b  | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs
+check exp obs
+rm exp obs
+[[ $FAILURES -eq 0 ]] || exit 1;