Add method sam_open_write for opening a htsFile file for writing only and setting a header to it.

Add getter methods hts_get_hdr, hts_get_fn.

Author: valeriuo

hts.c

@@ -1242,6 +1242,16 @@ const htsFormat *hts_get_format(htsFile *fp)
     return fp? &fp->format : NULL;
 }
 
+const struct sam_hdr_t *hts_get_hdr(htsFile *fp)
+{
+    return fp? fp->bam_header : 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 +508,22 @@ int hts_close(htsFile *fp);
 HTSLIB_EXPORT
 const htsFormat *hts_get_format(htsFile *fp);
 
+/*!
+  @abstract  Returns the file's header field
+  @param fp  The file handle
+  @return    Read-only pointer to the file's bam_header field.
+*/
+HTSLIB_EXPORT
+const struct sam_hdr_t *hts_get_hdr(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

@@ -1325,6 +1325,20 @@ 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);
 

sam.c

@@ -1671,6 +1671,30 @@ 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;