From 940ee181e97e4d93d392b3c8b50f6baf840b8937 Mon Sep 17 00:00:00 2001
From: Hao Hou <haohou302@gmail.com>
Date: Thu, 12 Dec 2019 11:38:08 -0700
Subject: [PATCH 1/2] Fix issue #803 and add test cases

---
 src/utils/BamTools/include/SamHeader.hpp |  5 +++--
 test/intersect/new_test-intersect.sh     | 12 ++++++++++++
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/utils/BamTools/include/SamHeader.hpp b/src/utils/BamTools/include/SamHeader.hpp
index 3a8bd6e9e..a4bdd5ddd 100644
--- 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
index 078b0f178..da9db4fa1 100755
--- 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;

From 47a35a1ed945de3db5fdb434f24600bc713ddc54 Mon Sep 17 00:00:00 2001
From: Hao Hou <haohou302@gmail.com>
Date: Thu, 12 Dec 2019 11:46:52 -0700
Subject: [PATCH 2/2] Make sure we also check all the PRs

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 43f5cac61..2e69c5e61 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,6 +1,6 @@
 name: CI
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   build: