fix up macos warnings

hasindu2008 · Sep 9, 2022 · 523c1ec · 523c1ec
1 parent fcead63
commit 523c1ec
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Showing 3 changed files with 67 additions and 80 deletions.
diff --git a/src/f5c.c b/src/f5c.c
@@ -24,6 +24,69 @@ Error counter for consecutive failures in the skip unreadable mode
 not all the memory allocations are needed for eventalign mode
 */
 
+//read bed file
+static inline char **read_bed_regions(char *bedfile, int64_t *count){
+
+    FILE *bedfp = fopen(bedfile,"r");
+    F_CHK(bedfp,bedfile);
+
+    char* buffer = (char*)malloc(sizeof(char) * (100)); //READ+newline+nullcharacter
+    MALLOC_CHK(buffer);
+
+    int64_t reg_capcacity = 1024;
+    int64_t reg_i = 0;
+    char **reg_list = (char **)malloc(reg_capcacity * sizeof(char *));
+    MALLOC_CHK(reg_list);
+
+
+    size_t bufferSize = 100;
+    ssize_t readlinebytes = 0;
+    int64_t line_no = 0;
+
+
+    while ((readlinebytes = getline(&buffer, &bufferSize, bedfp)) != -1) {
+
+        char *ref = (char *)malloc(sizeof(char)*readlinebytes);
+        MALLOC_CHK(ref);
+        int64_t beg=-1;
+        int64_t end=-1;
+
+        //TODO can optimised though strtok etc later
+        int ret=sscanf(buffer,"%s\t%ld\t%ld",ref,&beg, &end);
+        if(ret!=3 || end<beg){
+            ERROR("Malformed bed entry at line %ld",line_no);
+            exit(EXIT_FAILURE);
+        }
+
+        if(reg_i>=reg_capcacity){
+            if(reg_capcacity>1000000){
+                WARNING("The region bed file has over %ld regions. To reduce memory usage, you may consider merging bed regions.",reg_i);
+            }
+            reg_capcacity=reg_capcacity*2;
+            reg_list = (char **)realloc((void *)reg_list,reg_capcacity * sizeof(char *));
+            MALLOC_CHK(reg_list);
+
+        }
+
+        reg_list[reg_i] = (char *)malloc(sizeof(char)*readlinebytes);
+        sprintf(reg_list[reg_i],"%s:%ld-%ld",ref, beg, end);
+        reg_i++;
+
+
+        free(ref);
+
+
+
+        line_no++;
+    }
+
+    fclose(bedfp);
+    free(buffer);
+    *count = reg_i;
+
+    return reg_list;
+}
+
 /* initialise the core data structure */
 core_t* init_core(const char* bamfilename, const char* fastafile,
                   const char* fastqfile, const char* tmpfile, opt_t opt,double realtime0, int8_t mode, char *eventalignsummary, char *slow5file) {

diff --git a/src/f5cmisc.h b/src/f5cmisc.h
@@ -172,70 +172,6 @@ static inline void replace_char(char *str, char u, char t){
     }
 }
 
-//read bed file
-
-static inline char **read_bed_regions(char *bedfile, int64_t *count){
-
-    FILE *bedfp = fopen(bedfile,"r");
-    F_CHK(bedfp,bedfile);
-
-    char* buffer = (char*)malloc(sizeof(char) * (100)); //READ+newline+nullcharacter
-    MALLOC_CHK(buffer);
-
-    int64_t reg_capcacity = 1024;
-    int64_t reg_i = 0;
-    char **reg_list = (char **)malloc(reg_capcacity * sizeof(char *));
-    MALLOC_CHK(reg_list);
-
-
-    size_t bufferSize = 100;
-    ssize_t readlinebytes = 0;
-    int64_t line_no = 0;
-
-
-    while ((readlinebytes = getline(&buffer, &bufferSize, bedfp)) != -1) {
-
-        char *ref = (char *)malloc(sizeof(char)*readlinebytes);
-        MALLOC_CHK(ref);
-        int64_t beg=-1;
-        int64_t end=-1;
-
-        //TODO can optimised though strtok etc later
-        int ret=sscanf(buffer,"%s\t%ld\t%ld",ref,&beg, &end);
-        if(ret!=3 || end<beg){
-            ERROR("Malformed bed entry at line %ld",line_no);
-            exit(EXIT_FAILURE);
-        }
-
-        if(reg_i>=reg_capcacity){
-            if(reg_capcacity>1000000){
-                WARNING("The region bed file has over %ld regions. To reduce memory usage, you may consider merging bed regions.",reg_i);
-            }
-            reg_capcacity=reg_capcacity*2;
-            reg_list = (char **)realloc((void *)reg_list,reg_capcacity * sizeof(char *));
-            MALLOC_CHK(reg_list);
-
-        }
-
-        reg_list[reg_i] = (char *)malloc(sizeof(char)*readlinebytes);
-        sprintf(reg_list[reg_i],"%s:%ld-%ld",ref, beg, end);
-        reg_i++;
-
-
-        free(ref);
-
-
-
-        line_no++;
-    }
-
-    fclose(bedfp);
-    free(buffer);
-    *count = reg_i;
-
-    return reg_list;
-}
-
 static inline int64_t mm_parse_num(const char* str) //taken from minimap2
 {
     double x;

diff --git a/src/resquiggle.c b/src/resquiggle.c
@@ -141,11 +141,6 @@ core_t* init_core_rsq(opt_t opt, const char *slow5file, double realtime0) {
     }
     core->kmer_size = kmer_size;
 
-
-
-
-
-
     //realtime0
     core->realtime0=realtime0;
 
@@ -282,7 +277,6 @@ void free_db_tmp_rsq(db_t* db) {
 }
 
 
-
 //high similarity with f5c.c - can be modularised
 void process_db_rsq(core_t* core, db_t* db) {
 
@@ -404,20 +398,18 @@ void output_db_rsq(core_t* core, db_t* db, int8_t fmt) {
                     if(signal_start_point<0){
                         printf(".\t");
                     } else {
-                        printf("%ld\t", signal_start_point);
+                        printf("%ld\t", (long)signal_start_point);
                     }
                     if(signal_end_point<0){
                         printf(".\t");
                     } else {
-                        printf("%ld", signal_end_point);
+                        printf("%ld", (long)signal_end_point);
                     }
                     printf("\n");
                     if(signal_start_point>=0 && signal_end_point>=0){
                         if(signal_end_point<=signal_start_point){
                             fprintf(stderr,"ERROR: signal_end_point(%ld)<=signal_start_point(%ld)\n",signal_end_point,signal_start_point);
                             fprintf(stderr,"read_id=%s\tj=%d\tstartevent=%d\tendevent=%d\n",db->read_id[i],j,start_event_idx,end_event_idx);
-                            fprintf(stderr,"startevent.start=%ld\tstartevent.length=%f\tendevent.start=%ld\tendevent.length=%f\n",
-                                    et.event[start_event_idx].start,et.event[start_event_idx].length,et.event[end_event_idx].start,et.event[end_event_idx].length);
                             exit(EXIT_FAILURE);
                         }
                     }
@@ -434,9 +426,9 @@ void output_db_rsq(core_t* core, db_t* db, int8_t fmt) {
                 assert(signal_start_point2!=-1);
                 assert(signal_end_point2!=-1);
                 //query: name, start, end, strand
-                printf("%s\t%ld\t%ld\t%ld\t+\t", db->read_id[i], (long)db->sig[i]->nsample,signal_start_point2, signal_end_point2);
+                printf("%s\t%ld\t%ld\t%ld\t+\t", db->read_id[i], (long)db->sig[i]->nsample,(long)signal_start_point2, (long)signal_end_point2);
                 //target: name, start, end
-                printf("%s\t%d\t%ld\t%ld\t", db->read_id[i], n_kmers,rna?n_kmers-read_start:read_start, rna?n_kmers-1-read_end:read_end+1);
+                printf("%s\t%d\t%ld\t%ld\t", db->read_id[i], n_kmers,(long)(rna?n_kmers-read_start:read_start), (long)(rna?n_kmers-1-read_end:read_end+1));
                 //residue matches, block len, mapq
                 printf("%d\t%d\t%d\t",matches,n_kmers,255);
                 printf("sc:f:%f\t",db->scalings->scale);
@@ -513,10 +505,8 @@ static void read_slow5_single(core_t* core, db_t* db, int i){
         slow5_rec_free(record);
     }
 
-
 }
 
-
 ret_status_t load_db_rsq(core_t* core, db_t* db, gzFile fp, kseq_t *seq) {
 
     double load_start = realtime();
@@ -561,7 +551,6 @@ ret_status_t load_db_rsq(core_t* core, db_t* db, gzFile fp, kseq_t *seq) {
 
     core->db_fasta_time += realtime() - t;
 
-
     db->n_bam_rec = i;
     status.num_reads = i;
 
@@ -706,7 +695,6 @@ int resquiggle_main(int argc, char **argv) {
         exit(EXIT_FAILURE);
     }
 
-
     WARNING("%s","f5c resquiggle is experimental. Use with caution. Report any bugs under GitHub issues.");
 
     //open slow5