Check out-of-bound memory access, adds to b29c54c

samtools · Dec 3, 2024 · b482b77 · b482b77
1 parent d98d58f
commit b482b77
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Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/csq.c b/csq.c
@@ -1110,7 +1110,9 @@ fprintf(stderr,"splice_csq_del: %s>%s .. ex=%d,%d  beg,end=%d,%d  tbeg,tend=%d,%
                 {
                     if ( splice->check_donor && splice->tr->strand==STRAND_REV ) splice->csq |= CSQ_SPLICE_DONOR;
                     if ( splice->check_acceptor && splice->tr->strand==STRAND_FWD ) splice->csq |= CSQ_SPLICE_ACCEPTOR;
-                    if ( ref && alt && !strncmp(ref+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,alt+N_SPLICE_REGION_INTRON-N_SPLICE_DONOR,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
+
+                    int noff = N_SPLICE_REGION_INTRON - N_SPLICE_DONOR;
+                    if ( ref && alt && noff<splice->kref.l && noff<splice->kalt.l && !strncmp(ref+noff,alt+noff,N_SPLICE_DONOR) ) splice->csq |= CSQ_SYNONYMOUS_VARIANT;
                 }
             }
         }

diff --git a/test/csq/ENSCAFT00000047742/test.txt b/test/csq/ENSCAFT00000047742/test.txt
@@ -1,3 +1,3 @@
-104	CA	C	synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
-104	CA	C	synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
+104	CA	C	splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
+104	CA	C	splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
 
diff --git a/test/csq/ENSCAFT00000047742/test.vcf b/test/csq/ENSCAFT00000047742/test.vcf
@@ -4,4 +4,4 @@
 ##INFO=<ID=EXP,Number=1,Type=String,Description="Expected consequence">
 ##INFO=<ID=EXPL,Number=1,Type=String,Description="Expected consequence with bt/csq -l">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
-chr9	104	.	CA	C	.	PASS	EXP=synonymous&splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding
+chr9	104	.	CA	C	.	PASS	EXP=splice_acceptor&splice_donor|DUSP3|ENSCAFT00000047742|protein_coding