version with protection in out symbol

cobilab · Oct 28, 2024 · 6bc1ebe · 6bc1ebe
1 parent fc861b8
commit 6bc1ebe
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Showing 2 changed files with 30 additions and 6 deletions.
diff --git a/src/Jarvis3.c b/src/Jarvis3.c
@@ -52,6 +52,15 @@ int FindDataType(char *FN)
   return type;
   }
 
+// - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+// ERR AND EXIT ON UNKNOWN SYMBOL
+//
+void ErrAndExit(void)
+  {
+  fprintf(stderr, "Error: non ACGT symbol in sequence!\n");
+  exit(1);
+  }
+
 // - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 // ENCODE HEADER RMS ONLY
 //
@@ -254,8 +263,13 @@ void CompressRMsOnly(PARAM *P, char *fn)
 
   while((m = fread(t, sizeof(uint8_t), NSYM, IN)) == NSYM)
     {
+    if(!strchr("ACGT", t[0])) ErrAndExit();
+    if(!strchr("ACGT", t[1])) ErrAndExit();
+    if(!strchr("ACGT", t[2])) ErrAndExit();
+    if(!strchr("ACGT", t[3])) ErrAndExit();
+
     buf[i] = S2N(t[3])|(S2N(t[2])<<2)|(S2N(t[1])<<4)|(S2N(t[0])<<6); // PACK 4
-    
+
     for(n = 0 ; n < m ; ++n)
       {
       SB->buf[SB->idx] = sym = S2N(t[n]);
@@ -405,10 +419,15 @@ void CompressNoNN(PARAM *P, char *fn)
 
   while((m = fread(t, sizeof(uint8_t), NSYM, IN)) == NSYM)
     {
+    if(!strchr("ACGT", t[0])) ErrAndExit();
+    if(!strchr("ACGT", t[1])) ErrAndExit();
+    if(!strchr("ACGT", t[2])) ErrAndExit();
+    if(!strchr("ACGT", t[3])) ErrAndExit();
+
     buf[i] = S2N(t[3])|(S2N(t[2])<<2)|(S2N(t[1])<<4)|(S2N(t[0])<<6); // PACK 4
-
-    for(n = 0 ; n < m ; ++n){
 
+    for(n = 0 ; n < m ; ++n)
+      {
       SB->buf[SB->idx] = sym = S2N(t[n]);
 
       memset((void *)PT->freqs, 0, NSYM * sizeof(double));
@@ -629,10 +648,15 @@ void Compress(PARAM *P, char *fn){
 
   while((m = fread(t, sizeof(uint8_t), NSYM, IN)) == NSYM)
     {
-    buf[i] = S2N(t[3])|(S2N(t[2])<<2)|(S2N(t[1])<<4)|(S2N(t[0])<<6); // PACK 4
+    if(!strchr("ACGT", t[0])) ErrAndExit();
+    if(!strchr("ACGT", t[1])) ErrAndExit();
+    if(!strchr("ACGT", t[2])) ErrAndExit();
+    if(!strchr("ACGT", t[3])) ErrAndExit();
 
-    for(n = 0 ; n < m ; ++n){
+    buf[i] = S2N(t[3])|(S2N(t[2])<<2)|(S2N(t[1])<<4)|(S2N(t[0])<<6); // PACK 4
 
+    for(n = 0 ; n < m ; ++n)
+      {
       SB->buf[SB->idx] = sym = S2N(t[n]);
 
       memset((void *)PT->freqs, 0, NSYM * sizeof(double));

diff --git a/src/defs.h b/src/defs.h
@@ -71,7 +71,7 @@ PARAM;
 
 // - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 
-#define RELEASE                6
+#define RELEASE                7
 #define VERSION                3
 
 // - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -