[BUG] Failed to compile htslib.

[wjunLu]

When I used the following approach to compile lumpy-sv:

git clone --recursive git@github.com:arq5x/lumpy-sv.git
cd lumpy-sv
make

It failed on building htslib.

However, it succeeded when I changed the Makefile as follows:

diff --git a/Makefile b/Makefile
index 9b206fc..8b94c94 100644
--- a/Makefile
+++ b/Makefile
@@ -64,17 +64,17 @@ lumpy:
 		echo ""; \
 	done

-lumpy_filter: htslib
+lumpy_filter:
 	[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
 	$(MAKE) --no-print-directory -C src/filter/
 	cp src/filter/lumpy_filter $(BIN_DIR)


-htslib:
-	$(shell cd lib/htslib && autoreconf)
-	cd lib/htslib && \
-	./configure --disable-bz2 --disable-lzma --enable-libcurl
-	CFLAGS="$(CFLAGS) -DBGZF" $(MAKE) -C lib/htslib --no-print-directory CFLAGS="-DBGZF_MT"
+#htslib:
+#	cd lib/htslib && autoreconf
+#        cd lib/htslib && \
+#	./configure --disable-bz2 --disable-lzma --enable-libcurl
+#	CFLAGS="$(CFLAGS) -DBGZF" $(MAKE) -C lib/htslib --no-print-directory CFLAGS="-DBGZF_MT"

 lumpyexpress:
 	[ -d $(BIN_DIR) ] || mkdir -p $(BIN_DIR)
diff --git a/src/utils/BamTools/src/api/algorithms/Sort.h b/src/utils/BamTools/src/api/algorithms/Sort.h
index 32902e1..754df63 100644
--- a/src/utils/BamTools/src/api/algorithms/Sort.h
+++ b/src/utils/BamTools/src/api/algorithms/Sort.h
@@ -76,7 +76,7 @@ struct API_EXPORT Sort {
         { }

         // comparison function
-        bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) {
+        bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) const {
             return sort_helper(m_order, lhs.Name, rhs.Name);
         }

@@ -112,7 +112,7 @@ struct API_EXPORT Sort {
         { }

         // comparison function
-        bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) {
+        bool operator()(const BamTools::BamAlignment& lhs, const BamTools::BamAlignment& rhs) const {

             // force unmapped aligmnents to end
             if ( lhs.RefID == -1 ) return false;
diff --git a/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h b/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h
index 3000097..ceac8ed 100644
--- a/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h
+++ b/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h
@@ -61,7 +61,7 @@ struct MergeItemSorter : public std::binary_function<MergeItem, MergeItem, bool>
             : m_comp(comp)
         { }

-        bool operator()(const MergeItem& lhs, const MergeItem& rhs) {
+        bool operator()(const MergeItem& lhs, const MergeItem& rhs) const {
             const BamAlignment& l = *lhs.Alignment;
             const BamAlignment& r = *rhs.Alignment;
             return m_comp(l,r);

and pre-build htslib:

git clone --recursive git@github.com:arq5x/lumpy-sv.git
cd lumpy-sv
cd lib/htslib
./configure --disable-bz2 --disable-lzma --enable-libcurl
cd -
make

Above patch also shows another bugfix when gcc version is higher, const must be declared.