Allow sam_write1 to take a NULL header parameter.

Decouple htsFile::fnidx from its source and let HTSlib manage its memory.
Add method sam_open_write for opening a htsFile file for writing only and
setting a header to it.
Add getter method hts_get_fn.

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((void *)fp->fnidx);
     free(fp->line.s);
     free(fp);
     errno = save;
@@ -1242,6 +1243,11 @@ const htsFormat *hts_get_format(htsFile *fp)
     return fp? &fp->format : NULL;
 }
 
+const char *hts_get_fn(htsFile *fp)
+{
+    return fp? fp->fn : NULL;
+}
+
 const char *hts_format_file_extension(const htsFormat *format) {
     if (!format)
         return "?";

htslib/hts.h

@@ -508,6 +508,14 @@ int hts_close(htsFile *fp);
 HTSLIB_EXPORT
 const htsFormat *hts_get_format(htsFile *fp);
 
+/*!
+  @abstract  Returns the file's name
+  @param fp  The file handle
+  @return    Read-only pointer to the file's fn field.
+*/
+HTSLIB_EXPORT
+const char *hts_get_fn(htsFile *fp);
+
 /*!
   @ abstract      Returns a string containing the file format extension.
   @ param format  Format structure containing the file type.

htslib/sam.h

@@ -1089,8 +1089,7 @@ int bam_set_qname(bam1_t *b, const char *qname);
 /** @param fp        File handle for the data file being written.
     @param h         Bam header structured (needed for BAI and CSI).
     @param min_shift 0 for BAI, or larger for CSI (CSI defaults to 14).
-    @param fnidx     Filename to write index to.  This pointer must remain valid
-                     until after sam_idx_save is called.
+    @param fnidx     Filename to write index to.
     @return          0 on success, <0 on failure.
 
     @note This must be called after the header has been written, but before
@@ -1325,6 +1324,20 @@ const char *sam_parse_region(sam_hdr_t *h, const char *s, int *tid,
                              const char *mode,
                              const char *format);
 
+/// sam_open_write - Open a file for writing only
+/** The method opens a new alignment file for writing, writes header hdr to it
+ *  and attaches the header struct to the returned htsFile struct.
+ *  If successful, ownership of hdr is given to the htsFile struct and hdr
+ *  should not be freed separately.
+ *  @param fn      Name of the file
+ *  @param h       Pointer to the header previously read or created
+ *  @param mode    Pointer to the mode string (must contain "w")
+ *  @param fmt     Pointer to the format
+ *  @return        Pointer to the htsFile (with hdr) on success, NULL on failure
+ */
+    HTSLIB_EXPORT
+    htsFile *sam_open_write(const char *fn, sam_hdr_t *hdr, const char *mode, const htsFormat *fmt);
+
     HTSLIB_EXPORT
     int sam_hdr_change_HD(sam_hdr_t *h, const char *key, const char *val);
 
@@ -1343,7 +1356,8 @@ const char *sam_parse_region(sam_hdr_t *h, const char *s, int *tid,
     int sam_read1(samFile *fp, sam_hdr_t *h, bam1_t *b) HTS_RESULT_USED;
 /// sam_write1 - Write a record to a file
 /** @param fp    Pointer to the destination file
- *  @param h     Pointer to the header structure previously read
+ *  @param h     Pointer to the header structure previously read. Can be NULL,
+ *               if fp has a non-NULL pointer to a valid header struct.
  *  @param b     Pointer to the record to be written
  *  @return >= 0 on successfully writing the record, -1 on error
  */

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;
@@ -1671,6 +1673,30 @@ int sam_hdr_write(htsFile *fp, const sam_hdr_t *h)
     return 0;
 }
 
+htsFile *sam_open_write(const char *fn, sam_hdr_t *hdr, const char *mode, const htsFormat *fmt) {
+    htsFile *sf = NULL;
+    if (fn && mode) {
+        if (strchr(mode, 'w')) {
+            sf = hts_open_format(fn, mode, fmt);
+            if (sf) {
+                if (sam_hdr_write(sf, hdr) < 0) {
+                    hts_log_error("Writing header to file \"%s\" failed", fn);
+                    sam_close(sf);
+                    sf = NULL;
+                } else {
+                    if (sf->bam_header)
+                        sam_hdr_destroy(sf->bam_header);
+                    sf->bam_header = hdr;
+                }
+            }
+        } else {
+            hts_log_error("Only write mode allowed");
+        }
+    }
+
+    return sf;
+}
+
 static int old_sam_hdr_change_HD(sam_hdr_t *h, const char *key, const char *val)
 {
     char *p, *q, *beg = NULL, *end = NULL, *newtext;
@@ -3192,8 +3218,10 @@ int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
 
 // Sadly we need to be able to modify the bam_hdr here so we can
 // reference count the structure.
-int sam_write1(htsFile *fp, const sam_hdr_t *h, const bam1_t *b)
+int sam_write1(htsFile *fp, const sam_hdr_t *hdr, const bam1_t *b)
 {
+    const sam_hdr_t *h = hdr;
+    if (!h) h = fp->bam_header;
     switch (fp->format.format) {
     case binary_format:
         fp->format.category = sequence_data;

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;
 }