From 119ffec333923f0339b96a42b66ad3f5a5d19b27 Mon Sep 17 00:00:00 2001
From: sirus20x6 <sirus20x6@users.noreply.github.com>
Date: Wed, 25 Mar 2026 19:01:52 -0500
Subject: [PATCH] Fix missing header finalization and unchecked faidx_fetch_seq
 return

In gensample_to_vcf (vcfconvert.c), add the missing
bcf_hdr_add_sample(header, NULL) finalization call after the sample
addition loop, matching the pattern used in haplegendsample_to_vcf
and other converters.

In indel_ctx_type (vcfstats.c), check faidx_fetch_seq return for NULL
before dereferencing. If the chromosome is absent from the reference,
return the default indel length with nrep=0, nlen=0 instead of
crashing with a NULL pointer dereference.
---
 vcfconvert.c | 1 +
 vcfstats.c   | 6 ++++++
 2 files changed, 7 insertions(+)

diff --git a/vcfconvert.c b/vcfconvert.c
index 7b14d43c5..c46d9c72f 100644
--- a/vcfconvert.c
+++ b/vcfconvert.c
@@ -489,6 +489,7 @@ static void gensample_to_vcf(args_t *args)
         *se = 0;
         bcf_hdr_add_sample(args->header,samples[i]);
     }
+    bcf_hdr_add_sample(args->header,NULL);
     for (i=0; i<nsamples; i++) free(samples[i]);
     free(samples);
 
diff --git a/vcfstats.c b/vcfstats.c
index 09986b26a..ad4b19cb0 100644
--- a/vcfstats.c
+++ b/vcfstats.c
@@ -309,6 +309,12 @@ int indel_ctx_type(indel_ctx_t *ctx, char *chr, int pos, char *ref, char *alt, i
 
     int i, fai_ref_len;
     char *fai_ref = faidx_fetch_seq(ctx->ref, chr, pos-1, pos+win_size, &fai_ref_len);
+    if ( !fai_ref )
+    {
+        *nrep = 0;
+        *nlen = 0;
+        return alt_len - ref_len;
+    }
     for (i=0; i<fai_ref_len; i++)
         if ( (int)fai_ref[i]>96 ) fai_ref[i] -= 32;