From bb1e6b82de2b63765ba8e0c856118340f476637c Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 26 Aug 2021 12:22:45 +0100
Subject: [PATCH] Don't bail on symbolic ALTs

which can be veru long, just trim the maximum number of annotation
lines in the buffer.
---
 vcfannotate.c | 1 +
 1 file changed, 1 insertion(+)

diff --git a/vcfannotate.c b/vcfannotate.c
index eb79f507e..3db9e11c9 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -2921,6 +2921,7 @@ static void buffer_annot_lines(args_t *args, bcf1_t *line, int start_pos, int en
 
     while ( !bcf_sr_regions_overlap(args->tgts, bcf_seqname(args->hdr,line), start_pos,end_pos) )
     {
+        if ( args->nalines + 1 == 0xffff ) break;   // likely a symbolic allele, don't let the buffer overflow
         args->nalines++;
         hts_expand0(annot_line_t,args->nalines,args->malines,args->alines);
         annot_line_t *tmp = &args->alines[args->nalines-1];