Add ref_internal.h and correct ref.h

Author: ThomasHickman

Makefile

@@ -178,6 +178,7 @@ cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)
 cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) cram/string_alloc.h $(htslib_khash_h)
 cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
 hfile_internal_h = hfile_internal.h $(htslib_hfile_h)
+ref_internal_h = ref_internal.h $(htslib_hfile_h) cram/mFILE.h
 hts_internal_h = hts_internal.h $(htslib_hts_h)
 thread_pool_internal_h = thread_pool_internal.h $(htslib_thread_pool_h)
 
@@ -315,14 +316,14 @@ plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
 probaln.o probaln.pico: probaln.c config.h $(htslib_hts_h)
 realn.o realn.pico: realn.c config.h $(htslib_hts_h) $(htslib_sam_h)
 textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstring_h) $(hts_internal_h)
-ref.o ref.pico: ref.c config.h $(htslib_kstring_h) $(htslib_bgzf_h) $(cram_h) $(cram_io_h) $(cram_open_trace_file_h) $(htslib_hfile_h)
+ref.o ref.pico: ref.c config.h $(ref_internal_h) $(htslib_kstring_h) $(htslib_bgzf_h) $(cram_h) $(cram_io_h) $(cram_open_trace_file_h) $(htslib_hfile_h)
 
 cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
 cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h)
 cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_hts_endian_h)
 cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
 cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(hts_internal_h) $(cram_h) $(cram_os_h)
-cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h os/lzma_stub.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_ref_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) $(hts_internal_h)
+cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h os/lzma_stub.h $(ref_internal_h) $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_ref_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) $(hts_internal_h)
 cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)
 cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
 cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)

cram/cram_io.c

@@ -73,6 +73,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "cram/os.h"
 #include "htslib/hts.h"
 #include "htslib/ref.h"
+#include "ref_internal.h"
 #include "cram/open_trace_file.h"
 #include "cram/rANS_static.h"
 

htslib.mk

@@ -100,6 +100,7 @@ HTSLIB_ALL = \
 	$(HTSDIR)/realn.c \
 	$(HTSDIR)/regidx.c \
 	$(HTSDIR)/ref.c \
+	$(HTSDIR)/ref_internal.h \
 	$(HTSDIR)/sam.c \
 	$(HTSDIR)/synced_bcf_reader.c \
 	$(HTSDIR)/tbx.c \

htslib/ref.h

@@ -24,8 +24,8 @@ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.  */
 
 
-#ifndef HTSLIB_VCF_H
-#define HTSLIB_VCF_H
+#ifndef HTSLIB_REF_H
+#define HTSLIB_REF_H
 
 #include "bgzf.h"
 #include "htslib/hfile.h"
@@ -34,15 +34,6 @@ DEALINGS IN THE SOFTWARE.  */
 extern "C" {
 #endif
 
-typedef struct {
-    hFILE_wrapper base;
-    hFILE* innerhf;
-    int length;
-    char* file_name;
-    void* mf;
-    int is_mem_hfile;
-} hFILE_ref;
-
 /* m5_to_ref() - populates the ref parameter with the reference genome
  * for a given m5 string
  * @param m5_str: The m5 string to query

ref.c

@@ -38,6 +38,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #include "cram/open_trace_file.h"
 #include "htslib/hfile.h"
 #include "htslib/ref.h"
+#include "ref_internal.h"
 #include "hfile_internal.h"
 
 #include <errno.h>

ref_internal.h

@@ -0,0 +1,54 @@
+/// @file ref_internal.h
+/// Internal declarations from ref.c
+/*
+    Copyright (C) 2017 Genome Research Ltd.
+
+    Author: Thomas Hickman <[email protected]>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+
+#ifndef REF_INTERNAL_H
+#define REF_INTERNAL_H
+
+#include "htslib/hfile.h"
+#include "cram/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**
+ * Internal struct containing information about hFILEs created by m5_to_ref. Intended to be
+ * consumed by cram_populate_ref
+ */
+typedef struct {
+    hFILE_wrapper base;
+    int length;
+    char* file_name; // NOTE: this is set to NULL if this is an in-memory hFILE
+    mFILE* mf;
+    int is_mem_hfile;
+} hFILE_ref;
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif