Add methods sam_hdr_get and sam_hdr_set

htslib/sam.h

@@ -1,7 +1,7 @@
 /// @file htslib/sam.h
 /// High-level SAM/BAM/CRAM sequence file operations.
 /*
-    Copyright (C) 2008, 2009, 2013-2019 Genome Research Ltd.
+    Copyright (C) 2008, 2009, 2013-2020 Genome Research Ltd.
     Copyright (C) 2010, 2012, 2013 Broad Institute.
 
     Author: Heng Li <[email protected]>
@@ -818,6 +818,27 @@ char *stringify_argv(int argc, char *argv[]);
 HTSLIB_EXPORT
 void sam_hdr_incr_ref(sam_hdr_t *h);
 
+/// Gets the inner header from the sam file
+HTSLIB_EXPORT
+const sam_hdr_t *sam_hdr_get(samFile *f);
+
+/// Sets the header of the sam file
+/*!
+ * The method sets samFile::bam_header to the new hdr, following the replace
+ * policy (1 - replace the old header, 0 - keep the old header, if there is
+ * one).
+ *
+ * If the new header struct (hdr) is attached to f, its memory will be freed
+ * by sam_close, so the user must not attempt to free hdr separately.
+ *
+ * @param f        SAM/BAM/CRAM file structure
+ * @param hdr      Detached header structure to be set to f
+ * @param replace  1 - replace the old header, 0 - keep the old header
+ * @return         -1 on failure, 0 header not replaced, 1 header replaced
+ */
+HTSLIB_EXPORT
+int sam_hdr_set(samFile *f, sam_hdr_t *hdr, int replace);
+
 /*
  * Macros for changing the \@HD line. They eliminate the need to use NULL method arguments.
  */

sam.c

@@ -1,6 +1,6 @@
 /*  sam.c -- SAM and BAM file I/O and manipulation.
 
-    Copyright (C) 2008-2010, 2012-2019 Genome Research Ltd.
+    Copyright (C) 2008-2010, 2012-2020 Genome Research Ltd.
     Copyright (C) 2010, 2012, 2013 Broad Institute.
 
     Author: Heng Li <[email protected]>
@@ -1671,6 +1671,24 @@ int sam_hdr_write(htsFile *fp, const sam_hdr_t *h)
     return 0;
 }
 
+const sam_hdr_t *sam_hdr_get(samFile *f) {
+    sam_hdr_t *hdr = NULL;
+    if (f) hdr = f->bam_header;
+
+    return hdr;
+}
+
+int sam_hdr_set(samFile *f, sam_hdr_t *hdr, int replace) {
+    if (!f) return -1;
+    if (f->bam_header) {
+        if (replace) sam_hdr_destroy(f->bam_header);
+        else return 0;
+    }
+    f->bam_header = hdr;
+
+    return 1;
+}
+
 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;