From 799429155aef0debfe302c74847102b2971d40fc Mon Sep 17 00:00:00 2001
From: Rob Davies <rmd+git@sanger.ac.uk>
Date: Mon, 18 Sep 2023 16:27:21 +0100
Subject: [PATCH] Fix BCF/VCF on-the-fly indexing issues

* Switch from hts_idx_push() to bgzf_idx_push() for on-the-fly
  indexing of BCF and VCF.bgz files.  The latter function is
  needed to record the correct offsets when using multi-threaded
  BGZF compression.

  Fixes samtools/bcftools#1985

* Only allow indexing of BGZF-compressed files.  It's necessary to
  enforce this as on-the-fly indexing assumes that the file
  pointer is in htsFile::fp.bgzf, but uncompressed VCF uses
  htsFile::fp.hfile.
---
 vcf.c | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/vcf.c b/vcf.c
index 3bc7ef607..301d818cf 100644
--- a/vcf.c
+++ b/vcf.c
@@ -2236,7 +2236,8 @@ int bcf_write(htsFile *hfp, bcf_hdr_t *h, bcf1_t *v)
     if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1;
 
     if (hfp->idx) {
-        if (hts_idx_push(hfp->idx, v->rid, v->pos, v->pos + v->rlen, bgzf_tell(fp), 1) < 0)
+        if (bgzf_idx_push(fp, hfp->idx, v->rid, v->pos, v->pos + v->rlen,
+                          bgzf_tell(fp), 1) < 0)
             return -1;
     }
 
@@ -4184,19 +4185,19 @@ int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
     if ( fp->format.compression!=no_compression ) {
         if (bgzf_flush_try(fp->fp.bgzf, fp->line.l) < 0)
             return -1;
-        if (fp->idx)
-            hts_idx_amend_last(fp->idx, bgzf_tell(fp->fp.bgzf));
         ret = bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l);
     } else {
         ret = hwrite(fp->fp.hfile, fp->line.s, fp->line.l);
     }
 
-    if (fp->idx) {
+    if (fp->idx && fp->format.compression == bgzf) {
         int tid;
         if ((tid = hts_idx_tbi_name(fp->idx, v->rid, bcf_seqname_safe(h, v))) < 0)
             return -1;
 
-        if (hts_idx_push(fp->idx, tid, v->pos, v->pos + v->rlen, bgzf_tell(fp->fp.bgzf), 1) < 0)
+        if (bgzf_idx_push(fp->fp.bgzf, fp->idx,
+                          tid, v->pos, v->pos + v->rlen,
+                          bgzf_tell(fp->fp.bgzf), 1) < 0)
             return -1;
     }
 
@@ -4385,6 +4386,11 @@ static int vcf_idx_init(htsFile *fp, bcf_hdr_t *h, int min_shift, const char *fn
 int bcf_idx_init(htsFile *fp, bcf_hdr_t *h, int min_shift, const char *fnidx) {
     int n_lvls, nids = 0;
 
+    if (fp->format.compression != bgzf) {
+        hts_log_error("Indexing is only supported on BGZF-compressed files");
+        return -3; // Matches no-compression return for bcf_index_build3()
+    }
+
     if (fp->format.format == vcf)
         return vcf_idx_init(fp, h, min_shift, fnidx);