Add a new function to deal with makeing the index.

htslib/vcf.h

@@ -516,9 +516,25 @@ set to one of BCF_ERR* codes and must be checked before calling bcf_write().
     */
     HTSLIB_EXPORT
     int vcf_write_line(htsFile *fp, kstring_t *line);
-
+
+
+
+    /// Write a line to a VCF file for indexing
+    /** @param line   Line to write
+        @param fp     File to write it to
+        @param h      The header for the vcf file
+        @param chr_id Chromosome id
+        @param name   Chromosome name
+        @param beg    Beginning position
+        @param end    End position
+        @return 0 on success; -1 on failure
+
+        @note Similar to vcf_write_line.  No checks are done on the line being added, apart from
+              ensuring that it ends with a newline.  This function
+              should therefore be used with care.
+    */
     HTSLIB_EXPORT
-    int vcf_write_line_with_index(htsFile *fp, const bcf_hdr_t *h, kstring_t *line, int tid, hts_pos_t pos, hts_pos_t len);
+    int vcf_write_line_with_index(htsFile *fp, const bcf_hdr_t *h, kstring_t *line, int chr_id, char *name, hts_pos_t pos, hts_pos_t len);
 
     /**************************************************************************
      *  Header querying and manipulation routines

vcf.c

@@ -4258,28 +4258,31 @@ int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
 }
 
 
-int vcf_write_line_with_index(htsFile *fp,  const bcf_hdr_t *h, kstring_t *line, int tid,
-            hts_pos_t pos, hts_pos_t len)
+int vcf_write_line_with_index(htsFile *fp,  const bcf_hdr_t *h, kstring_t *line, int chr_id,
+            char *name, hts_pos_t pos, hts_pos_t len)
 {
     ssize_t ret;
-
-    fprintf(stderr, "vcf_write_line_with_index start\n");
 
     if (fp->format.compression == no_compression || !fp->idx) { // compressed reads only for indexing
         return -1;
     }
-
-    ret = bgzf_write(fp->fp.bgzf, line->s, line->l); // error handling?
-
+
+    kputs("\n", line);
+    ret = bgzf_write(fp->fp.bgzf, line->s, line->l);
+
+    int tid;
+
+    if ((tid = hts_idx_tbi_name(fp->idx, chr_id, name)) < 0) {
+        return -1;
+    }
+
     if (bgzf_idx_push(fp->fp.bgzf, fp->idx, tid, pos, pos + len, bgzf_tell(fp->fp.bgzf), 1) < 0) {
         return -1;
     }
-
-    fprintf(stderr, "vcf_write_line_with_index end\n");
-
-    return 0; // again, more error handling needed
+
+    return ret==line->l ? 0 : -1;
 }
-  
+
 
 /************************
  * Data access routines *