Decouple htsFile::fnidx from its source and let HTSlib manage its memory.

Author: valeriuo

hts.c

@@ -1231,6 +1231,7 @@ int hts_close(htsFile *fp)
     hts_idx_destroy(fp->idx);
     free(fp->fn);
     free(fp->fn_aux);
+    free(fp->fnidx);
     free(fp->line.s);
     free(fp);
     errno = save;

htslib/hts.h

@@ -238,7 +238,7 @@ typedef struct {
     void *state;  // format specific state information
     htsFormat format;
     hts_idx_t *idx;
-    const char *fnidx;
+    char *fnidx;
     struct sam_hdr_t *bam_header;
 } htsFile;
 

sam.c

@@ -894,7 +894,9 @@ int bam_index_build(const char *fn, int min_shift)
 // Initialise fp->idx for the current format type.
 // This must be called after the header has been written but no other data.
 int sam_idx_init(htsFile *fp, sam_hdr_t *h, int min_shift, const char *fnidx) {
-    fp->fnidx = fnidx;
+    fp->fnidx = strdup(fnidx);
+    if (!fp->fnidx) return -1;
+
     if (fp->format.format == bam || fp->format.format == bcf ||
         (fp->format.format == sam && fp->format.compression == bgzf)) {
         int n_lvls, fmt = HTS_FMT_CSI;

vcf.c

@@ -3295,7 +3295,8 @@ static int vcf_idx_init(htsFile *fp, bcf_hdr_t *h, int min_shift, const char *fn
         fp->idx = NULL;
         return -1;
     }
-    fp->fnidx = fnidx;
+    fp->fnidx = strdup(fnidx);
+    if (!fp->fnidx) return -1;
 
     return 0;
 }
@@ -3315,7 +3316,8 @@ int bcf_idx_init(htsFile *fp, bcf_hdr_t *h, int min_shift, const char *fnidx) {
 
     fp->idx = hts_idx_init(nids, HTS_FMT_CSI, bgzf_tell(fp->fp.bgzf), min_shift, n_lvls);
     if (!fp->idx) return -1;
-    fp->fnidx = fnidx;
+    fp->fnidx = strdup(fnidx);
+    if (!fp->fnidx) return -1;
 
     return 0;
 }