Fixing the make issue related to disabling FAST5

src/Makefile

@@ -190,13 +190,13 @@ pod5: check_zstd
 		cd $(WORKDIR) && mkdir -p $(POD5_URLDIR); cd $(POD5_URLDIR); wget -qO- $(POD5_URL) | tar -xzv; \
 	fi
 
-ifeq ($(NOHDF5),1)
-FASTDEPCOM=${CC}
-FASTDEPCOM_FLAGS=$(CFLAGS)
-else
+# ifeq ($(NOHDF5),1)
+# FASTDEPCOM=${CC}
+# FASTDEPCOM_FLAGS=$(CFLAGS)
+# else
 FASTDEPCOM=${CXX}
 FASTDEPCOM_FLAGS=$(CPPFLAGS)
-endif
+# endif
 
 # $(PROG): $(OBJS)
 # 	${FASTDEPCOM} $(FASTDEPCOM_FLAGS) $(OBJS) -o $(PROG) $(LIBS)

src/rindex.c

@@ -34,8 +34,8 @@ typedef struct {
 	ri_idx_t* ri;
 
 	int n_f, cur_f; //number of files, index of the current file (in sf)
-	ri_sig_file_t *sfp; //pointer to the current fast5 file
-	char **sf; //fast5 file names (multi if directory is given, single if single file is given)
+	ri_sig_file_t *sfp; //pointer to the current signal file
+	char **sf; //signal file names (multi if directory is given, single if single file is given)
 } pipeline_t;
 
 typedef struct {

src/rindex.h

@@ -123,7 +123,7 @@ int64_t ri_idx_is_idx(const char* fn);
  * 
  * @return		rindex (index)
  */
-ri_idx_t* ri_idx_init(int b, int w, int e, int n, int q, int lq, int k, int flag);
+ri_idx_t* ri_idx_init(float diff, int b, int w, int e, int n, int q, int k, float fine_min, float fine_max, float fine_range, int flag);
 
 /**
  * Reads or constructs the index from file. If the file is not index, it should be a file containing sequences to generate the index for.

src/rsig.h

@@ -49,7 +49,6 @@ typedef struct ri_sig_file_s {
 	unsigned long int pod5_row;
 	#ifndef NPOD5RH
 	Pod5ReadRecordBatch_t* batch;
-
 	Pod5FileReader_t* pp; //POD5 file pointer
 	#endif