bcf_hdr_combine replaced by bcf_hdr_merge, fixes samtools/bcftools#208

htslib/vcf.h

@@ -376,13 +376,23 @@ typedef struct {
 
     /** Create a new header using the supplied template */
     bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr);
+
     /**
-     *  Copy header lines from src to dst if not already present in dst. See also bcf_translate().
-     *  Returns 0 on success or sets a bit on error:
-     *      1 .. conflicting definitions of tag length
-     *      // todo
+     *  bcf_hdr_merge() - copy header lines from src to dst, see also bcf_translate()
+     *  @param dst: the destination header to be merged into, NULL on the first pass
+     *  @param src: the source header
+     *
+     *  Notes:
+     *      - use as:
+     *          bcf_hdr_t *dst = NULL;
+     *          for (i=0; i<nsrc; i++) dst = bcf_hdr_merge(dst,src[i]);
+     *
+     *      - bcf_hdr_merge() replaces bcf_hdr_combine() which had a problem when
+     *      combining multiple BCF headers. The current bcf_hdr_combine() is
+     *      does not have this problem, but became slow when used for many files.
      */
-    int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src);
+    int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src);  // deprecated, do not use!
+    bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src);
 
     /**
      *  bcf_hdr_add_sample() - add a new sample.

vcf.c

@@ -2209,6 +2209,22 @@ int bcf_index_build(const char *fn, int min_shift)
 
 int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src)
 {
+    fprintf(stderr,"Please use bcf_hdr_merge instead, bcf_hdr_combine will be deprecated\n");
+    assert(0);  // todo
+}
+
+bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src)
+{
+    if ( !dst )
+    {
+        // this will effectively strip existing IDX attributes from src to become dst
+        dst = bcf_hdr_init("r");
+        char *htxt = bcf_hdr_fmt_text(src, 0, NULL);
+        bcf_hdr_parse(dst, htxt);
+        free(htxt);
+        return dst;
+    }
+
     int i, ndst_ori = dst->nhrec, need_sync = 0, ret = 0;
     for (i=0; i<src->nhrec; i++)
     {
@@ -2268,7 +2284,7 @@ int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src)
         }
     }
     if ( need_sync ) bcf_hdr_sync(dst);
-    return ret;
+    return dst;
 }
 int bcf_translate(const bcf_hdr_t *dst_hdr, bcf_hdr_t *src_hdr, bcf1_t *line)
 {