Check the return status of bcf_hdr_append()

to make sure the program does not produce invalid contig ids and tags.
Note that the check was added only in places relying on user input,
not the ones trivially true.

Resolves #2345

Author: pd3

mpileup.c

@@ -1,6 +1,6 @@
 /*  mpileup.c -- mpileup subcommand. Previously bam_plcmd.c from samtools
 
-    Copyright (C) 2008-2024 Genome Research Ltd.
+    Copyright (C) 2008-2025 Genome Research Ltd.
     Portions copyright (C) 2009-2012 Broad Institute.
 
     Author: Heng Li <[email protected]>
@@ -766,20 +766,20 @@ static int mpileup(mplp_conf_t *conf)
     if (conf->record_cmd_line)
     {
         ksprintf(&conf->buf, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
-        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+        if ( bcf_hdr_append(conf->bcf_hdr, conf->buf.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
 
         conf->buf.l = 0;
         ksprintf(&conf->buf, "##bcftoolsCommand=mpileup");
         for (i=1; i<conf->argc; i++) ksprintf(&conf->buf, " %s", conf->argv[i]);
         kputc('\n', &conf->buf);
-        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+        if ( bcf_hdr_append(conf->bcf_hdr, conf->buf.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
     }
 
     if (conf->fai_fname)
     {
         conf->buf.l = 0;
         ksprintf(&conf->buf, "##reference=file://%s\n", conf->fai_fname);
-        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+        if ( bcf_hdr_append(conf->bcf_hdr, conf->buf.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
     }
 
     // Translate BAM @SQ tags to BCF ##contig tags
@@ -788,7 +788,7 @@ static int mpileup(mplp_conf_t *conf)
     {
         conf->buf.l = 0;
         ksprintf(&conf->buf, "##contig=<ID=%s,length=%d>", hdr->target_name[i], hdr->target_len[i]);
-        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+        if ( bcf_hdr_append(conf->bcf_hdr, conf->buf.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
     }
     conf->buf.l = 0;
 

vcfannotate.c

@@ -2415,7 +2415,7 @@ static void init_columns(args_t *args)
                 col->hdr_key_dst = strdup(str.s+5);
                 tmp.l = 0;
                 ksprintf(&tmp,"##INFO=<ID=%s,Number=.,Type=String,Description=\"Transferred FILTER column\">",col->hdr_key_dst);
-                bcf_hdr_append(args->hdr_out, tmp.s);
+                if ( bcf_hdr_append(args->hdr_out, tmp.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
                 if (bcf_hdr_sync(args->hdr_out) < 0) error_errno("[%s] Failed to update header", __func__);
                 int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, col->hdr_key_dst);
                 col->number = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id);
@@ -2447,7 +2447,7 @@ static void init_columns(args_t *args)
                     if ( k<0 ) error("[%s] Failed to parse the header, the ID attribute not found", __func__);
                     tmp.l = 0;
                     bcf_hrec_format(hrec, &tmp);
-                    bcf_hdr_append(args->hdr_out, tmp.s);
+                    if ( bcf_hdr_append(args->hdr_out, tmp.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
                 }
                 if (bcf_hdr_sync(args->hdr_out) < 0)
                     error_errno("[%s] Failed to update header", __func__);
@@ -2481,7 +2481,7 @@ static void init_columns(args_t *args)
                 if ( skip_info && khash_str2int_has_key(skip_info,hrec->vals[k]) ) continue;
                 tmp.l = 0;
                 bcf_hrec_format(hrec, &tmp);
-                bcf_hdr_append(args->hdr_out, tmp.s);
+                if ( bcf_hdr_append(args->hdr_out, tmp.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
                 if (bcf_hdr_sync(args->hdr_out) < 0)
                     error_errno("[%s] Failed to update header", __func__);
                 int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]);
@@ -2517,7 +2517,7 @@ static void init_columns(args_t *args)
                 if ( skip_fmt && khash_str2int_has_key(skip_fmt,hrec->vals[k]) ) continue;
                 tmp.l = 0;
                 bcf_hrec_format(hrec, &tmp);
-                bcf_hdr_append(args->hdr_out, tmp.s);
+                if ( bcf_hdr_append(args->hdr_out, tmp.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
                 if (bcf_hdr_sync(args->hdr_out) < 0)
                     error_errno("[%s] Failed to update header", __func__);
                 int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, hrec->vals[k]);
@@ -2565,7 +2565,7 @@ static void init_columns(args_t *args)
                 if ( !hrec ) error("No such annotation \"%s\" in %s\n", key_src,args->targets_fname);
                 tmp.l = 0;
                 bcf_hrec_format_rename(hrec, key_dst, &tmp);
-                bcf_hdr_append(args->hdr_out, tmp.s);
+                if ( bcf_hdr_append(args->hdr_out, tmp.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
                 if (bcf_hdr_sync(args->hdr_out) < 0)
                     error_errno("[%s] Failed to update header", __func__);
             }
@@ -2698,7 +2698,7 @@ static void init_columns(args_t *args)
                         tmp.l = 0;
                         bcf_hrec_format_rename(hrec, key_dst, &tmp);
                     }
-                    bcf_hdr_append(args->hdr_out, tmp.s);
+                    if ( bcf_hdr_append(args->hdr_out, tmp.s) ) error("[%s:%d] failed to update the header\n",__FILE__,__LINE__);
                     if (bcf_hdr_sync(args->hdr_out) < 0)
                         error_errno("[%s] Failed to update header", __func__);
                     hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key_dst);