Allow sam_write1 to take a NULL header parameter.

Author: valeriuo

hts.c

@@ -1231,7 +1231,7 @@ int hts_close(htsFile *fp)
     hts_idx_destroy(fp->idx);
     free(fp->fn);
     free(fp->fn_aux);
-    free(fp->fnidx);
+    free((void *)fp->fnidx);
     free(fp->line.s);
     free(fp);
     errno = save;
@@ -1243,11 +1243,6 @@ 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;

htslib/hts.h

@@ -238,7 +238,7 @@ typedef struct {
     void *state;  // format specific state information
     htsFormat format;
     hts_idx_t *idx;
-    char *fnidx;
+    const char *fnidx;
     struct sam_hdr_t *bam_header;
 } htsFile;
 
@@ -508,14 +508,6 @@ 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

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
@@ -1357,7 +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

@@ -3218,8 +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;