Ensure HTSlib prefers its own headers when being compiled

cram/cram.h

@@ -42,8 +42,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #ifndef CRAM_ALL_H
 #define CRAM_ALL_H
 
-#include "cram/cram_samtools.h"
-#include "header.h"
+#include "cram_samtools.h"
+#include "../header.h"
 #include "cram_structs.h"
 #include "cram_io.h"
 #include "cram_encode.h"
@@ -56,6 +56,6 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 //
 // This contains duplicated portions from cram_io.h and cram_structs.h,
 // so we want to ensure that the prototypes match.
-#include "htslib/cram.h"
+#include "../htslib/cram.h"
 
 #endif

cram/cram_codecs.c

@@ -43,7 +43,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <stdint.h>
 #include <errno.h>
 
-#include "cram/cram.h"
+#include "cram.h"
 
 /*
  * ---------------------------------------------------------------------------

cram/cram_decode.c

@@ -48,9 +48,9 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <stdint.h>
 #include <inttypes.h>
 
-#include "cram/cram.h"
-#include "cram/os.h"
-#include "htslib/hts.h"
+#include "cram.h"
+#include "os.h"
+#include "../htslib/hts.h"
 
 //Whether CIGAR has just M or uses = and X to indicate match and mismatch
 //#define USE_X

cram/cram_encode.c

@@ -43,11 +43,11 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <math.h>
 #include <inttypes.h>
 
-#include "cram/cram.h"
-#include "cram/os.h"
-#include "sam_internal.h" // for nibble2base
-#include "htslib/hts.h"
-#include "htslib/hts_endian.h"
+#include "cram.h"
+#include "os.h"
+#include "../sam_internal.h" // for nibble2base
+#include "../htslib/hts.h"
+#include "../htslib/hts_endian.h"
 
 KHASH_MAP_INIT_STR(m_s2u64, uint64_t)
 

cram/cram_external.c

@@ -41,8 +41,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
 #include <config.h>
 
-#include "htslib/hfile.h"
-#include "cram/cram.h"
+#include "../htslib/hfile.h"
+#include "cram.h"
 
 /*
  *-----------------------------------------------------------------------------

cram/cram_index.c

@@ -62,11 +62,11 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <sys/stat.h>
 #include <math.h>
 
-#include "htslib/bgzf.h"
-#include "htslib/hfile.h"
-#include "hts_internal.h"
-#include "cram/cram.h"
-#include "cram/os.h"
+#include "../htslib/bgzf.h"
+#include "../htslib/hfile.h"
+#include "../hts_internal.h"
+#include "cram.h"
+#include "os.h"
 
 #if 0
 static void dump_index_(cram_index *e, int level) {

cram/cram_io.c

@@ -56,7 +56,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #ifdef HAVE_LZMA_H
 #include <lzma.h>
 #else
-#include "os/lzma_stub.h"
+#include "../os/lzma_stub.h"
 #endif
 #endif
 #include <sys/types.h>
@@ -70,11 +70,11 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #define crc32(a,b,c) libdeflate_crc32((a),(b),(c))
 #endif
 
-#include "cram/cram.h"
-#include "cram/os.h"
-#include "htslib/hts.h"
-#include "cram/open_trace_file.h"
-#include "cram/rANS_static.h"
+#include "cram.h"
+#include "os.h"
+#include "../htslib/hts.h"
+#include "open_trace_file.h"
+#include "rANS_static.h"
 
 //#define REF_DEBUG
 
@@ -87,10 +87,10 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #define RP(...)
 #endif
 
-#include "htslib/hfile.h"
-#include "htslib/bgzf.h"
-#include "htslib/faidx.h"
-#include "hts_internal.h"
+#include "../htslib/hfile.h"
+#include "../htslib/bgzf.h"
+#include "../htslib/faidx.h"
+#include "../hts_internal.h"
 
 #ifndef PATH_MAX
 #define PATH_MAX FILENAME_MAX

cram/cram_io.h

@@ -43,7 +43,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #define CRAM_IO_H
 
 #include <stdint.h>
-#include <cram/misc.h>
+
+#include "misc.h"
 
 #ifdef __cplusplus
 extern "C" {

cram/cram_samtools.c

@@ -35,8 +35,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <string.h>
 #include <stdlib.h>
 
-#include "cram/cram.h"
-#include "htslib/sam.h"
+#include "cram.h"
+#include "../htslib/sam.h"
 #include "../sam_internal.h"
 
 /*---------------------------------------------------------------------------

cram/cram_samtools.h

@@ -56,7 +56,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 #define bam_reg2bin(beg,end) hts_reg2bin((beg),(end),14,5)
 
-#include "htslib/sam.h"
+#include "../htslib/sam.h"
 
 enum cigar_op {
     BAM_CMATCH_=BAM_CMATCH,

cram/cram_stats.c

@@ -42,8 +42,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <math.h>
 #include <inttypes.h>
 
-#include "cram/cram.h"
-#include "cram/os.h"
+#include "cram.h"
+#include "os.h"
 
 cram_stats *cram_stats_create(void) {
     return calloc(1, sizeof(cram_stats));

cram/cram_structs.h

@@ -50,11 +50,11 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <stdint.h>
 #include <sys/types.h>
 
-#include "htslib/thread_pool.h"
-#include "htslib/cram.h"
-#include "cram/string_alloc.h"
-#include "cram/mFILE.h"
-#include "htslib/khash.h"
+#include "../htslib/thread_pool.h"
+#include "../htslib/cram.h"
+#include "string_alloc.h"
+#include "mFILE.h"
+#include "../htslib/khash.h"
 
 #ifdef __cplusplus
 extern "C" {

cram/mFILE.c

@@ -41,9 +41,9 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <unistd.h>
 #include <stdarg.h>
 
-#include "htslib/hts_log.h"
-#include "cram/os.h"
-#include "cram/mFILE.h"
+#include "../htslib/hts_log.h"
+#include "os.h"
+#include "mFILE.h"
 
 #ifdef HAVE_MMAP
 #include <sys/mman.h>

cram/open_trace_file.c

@@ -72,16 +72,17 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <errno.h>
 #include <sys/types.h>
 #include <sys/stat.h>
-#include "cram/os.h"
+
+#include "os.h"
 #ifndef PATH_MAX
 #  define PATH_MAX 1024
 #endif
 
-#include "cram/open_trace_file.h"
-#include "cram/misc.h"
-#include "htslib/hfile.h"
-#include "htslib/hts_log.h"
-#include "htslib/hts.h"
+#include "open_trace_file.h"
+#include "misc.h"
+#include "../htslib/hfile.h"
+#include "../htslib/hts_log.h"
+#include "../htslib/hts.h"
 
 /*
  * Returns whether the path refers to a regular file.

cram/open_trace_file.h

@@ -64,7 +64,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #ifndef OPEN_TRACE_FILE_H
 #define OPEN_TRACE_FILE_H
 
-#include "cram/mFILE.h"
+#include "mFILE.h"
 
 #ifdef __cplusplus
 extern "C" {

cram/os.h

@@ -77,7 +77,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 #include <limits.h>
 #include <stdint.h>
-#include "htslib/hts_endian.h"
+
+#include "../htslib/hts_endian.h"
 
 #ifdef __cplusplus
 extern "C" {

cram/pooled_alloc.c

@@ -35,8 +35,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <stdio.h>
 #include <stdint.h>
 
-#include "cram/pooled_alloc.h"
-#include "cram/misc.h"
+#include "pooled_alloc.h"
+#include "misc.h"
 
 //#define DISABLE_POOLED_ALLOC
 //#define TEST_MAIN

cram/rANS_static.c

@@ -47,8 +47,8 @@
 #include <sys/time.h>
 #include <limits.h>
 
-#include "cram/rANS_static.h"
-#include "cram/rANS_byte.h"
+#include "rANS_static.h"
+#include "rANS_byte.h"
 
 #define TF_SHIFT 12
 #define TOTFREQ (1<<TF_SHIFT)

cram/string_alloc.c

@@ -43,7 +43,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include <stdlib.h>
 #include <stdio.h>
 
-#include "cram/string_alloc.h"
+#include "string_alloc.h"
 
 #define MIN_STR_SIZE 1024
 

htslib/khash.h

@@ -129,8 +129,9 @@ int main() {
 #include <stdlib.h>
 #include <string.h>
 #include <limits.h>
-#include <htslib/kstring.h>
-#include <htslib/kroundup.h>
+
+#include "kstring.h"
+#include "kroundup.h"
 
 /* compiler specific configuration */
 

htslib/khash_str2int.h

@@ -25,7 +25,7 @@ DEALINGS IN THE SOFTWARE.  */
 #ifndef HTSLIB_KHASH_STR2INT_H
 #define HTSLIB_KHASH_STR2INT_H
 
-#include <htslib/khash.h>
+#include "khash.h"
 
 KHASH_MAP_INIT_STR(str2int, int)
 

test/fieldarith.c

@@ -26,7 +26,7 @@ DEALINGS IN THE SOFTWARE.  */
 
 #include <stdio.h>
 
-#include "htslib/sam.h"
+#include "../htslib/sam.h"
 
 int ntests = 0;
 int nfailures = 0;

test/fuzz/hts_open_fuzzer.c

@@ -31,10 +31,11 @@ DEALINGS IN THE SOFTWARE.  */
 #include <stdlib.h>
 #include <string.h>
 #include <unistd.h>
-#include "htslib/hfile.h"
-#include "htslib/hts.h"
-#include "htslib/sam.h"
-#include "htslib/vcf.h"
+
+#include "../../htslib/hfile.h"
+#include "../../htslib/hts.h"
+#include "../../htslib/sam.h"
+#include "../../htslib/vcf.h"
 
 static void hts_close_or_abort(htsFile* file) {
     if (hts_close(file) != 0) {

test/hfile.c

@@ -31,9 +31,9 @@ DEALINGS IN THE SOFTWARE.  */
 
 #include <sys/stat.h>
 
-#include "htslib/hfile.h"
-#include "htslib/hts_defs.h"
-#include "htslib/kstring.h"
+#include "../htslib/hfile.h"
+#include "../htslib/hts_defs.h"
+#include "../htslib/kstring.h"
 
 void HTS_NORETURN fail(const char *format, ...)
 {

test/hts_endian.c

@@ -28,7 +28,8 @@ DEALINGS IN THE SOFTWARE.  */
 #include <string.h>
 #include <stdint.h>
 #include <inttypes.h>
-#include "htslib/hts_endian.h"
+
+#include "../htslib/hts_endian.h"
 
 typedef struct {
     uint8_t u8[2];

test/pileup.c

@@ -47,8 +47,9 @@ samtools mpileup -B -Q 0 in.bam | perl -lane \
 #include <errno.h>
 #include <ctype.h>
 #include <unistd.h>
-#include "htslib/sam.h"
-#include "htslib/kstring.h"
+
+#include "../htslib/sam.h"
+#include "../htslib/kstring.h"
 
 #define MIN(a,b) ((a)<(b)?(a):(b))
 

test/sam.c

@@ -35,14 +35,14 @@ DEALINGS IN THE SOFTWARE.  */
 #include <unistd.h>
 
 // Suppress message for faidx_fetch_nseq(), which we're intentionally testing
-#include "htslib/hts_defs.h"
+#include "../htslib/hts_defs.h"
 #undef HTS_DEPRECATED
 #define HTS_DEPRECATED(message)
 
-#include "htslib/sam.h"
-#include "htslib/faidx.h"
-#include "htslib/khash.h"
-#include "htslib/hts_log.h"
+#include "../htslib/sam.h"
+#include "../htslib/faidx.h"
+#include "../htslib/khash.h"
+#include "../htslib/hts_log.h"
 
 KHASH_SET_INIT_STR(keep)
 typedef khash_t(keep) *keephash_t;

test/test-bcf-sr.c

@@ -32,7 +32,8 @@
 #include <stdio.h>
 #include <stdarg.h>
 #include <inttypes.h>
-#include <htslib/synced_bcf_reader.h>
+
+#include "../htslib/synced_bcf_reader.h"
 
 void error(const char *format, ...)
 {

test/test-bcf-translate.c

@@ -24,8 +24,10 @@
 */
 
 #include <config.h>
+
 #include <stdio.h>
-#include <htslib/vcf.h>
+
+#include "../htslib/vcf.h"
 
 void error(const char *format, ...)
 {