Accept .fa

thegenemyers · Sep 18, 2023 · 77f3a21 · 77f3a21
1 parent 8662b7d
commit 77f3a21
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Showing 3 changed files with 18 additions and 9 deletions.
diff --git a/ONElib.c b/ONElib.c
@@ -32,7 +32,7 @@
 #ifdef DEBUG
 #include <assert.h>
 #else
-#define assert(x) 0
+#define assert(x)
 #endif
 
 #include "ONElib.h"
@@ -390,9 +390,10 @@ static OneSchema *oneSchemaCreateDynamic (char *fileType, char *subType)
   assert (fileType && strlen(fileType) > 0) ;
   assert (!subType || strlen(subType) > 0) ;
   if (subType)
-    sprintf (text, "P %ld %s\nS %ld %s\n", strlen(fileType),fileType, strlen(subType), subType) ;
+    sprintf (text, "P %d %s\nS %d %s\n", (int) strlen(fileType),fileType,
+                                         (int) strlen(subType), subType) ;
   else
-    sprintf (text, "P %ld %s\n", strlen(fileType), fileType) ;
+    sprintf (text, "P %d %s\n", (int) strlen(fileType), fileType) ;
   OneSchema *vs = oneSchemaCreateFromText (text) ;
   return vs ;
 }
@@ -3485,7 +3486,7 @@ static inline int intGet (unsigned char *u, I64 *pval)
     case 0:
       switch (u[0] & 0x07)
 	{
-	case 0: die ("int packing error") ;
+	case 0: die ("int packing error") ; break ;
 	case 1: *pval = *(I64*)(u+1) & 0x0000000000ffff ; return 3 ;
 	case 2: *pval = *(I64*)(u+1) & 0x00000000ffffff ; return 4 ;
 	case 3: *pval = *(I64*)(u+1) & 0x000000ffffffff ; return 5 ;
@@ -3497,7 +3498,7 @@ static inline int intGet (unsigned char *u, I64 *pval)
     case 4:
       switch (u[0] & 0x07)
 	{
-	case 0: die ("int packing error") ;
+	case 0: die ("int packing error") ; break ;
 	case 1: *pval = *(I64*)(u+1) | 0xffffffffffff0000 ; return 3 ;
 	case 2: *pval = *(I64*)(u+1) | 0xffffffffff000000 ; return 4 ;
 	case 3: *pval = *(I64*)(u+1) | 0xffffffff00000000 ; return 5 ;

diff --git a/fasta2DAM.c b/fasta2DAM.c
@@ -358,8 +358,12 @@ int main(int argc, char *argv[])
 
             path  = PathTo(ng->name);
             core  = Root(ng->name,".fasta");
-            if ((input = Fopen(Catenate(path,"/",core,".fasta"),"r")) == NULL)
-              goto error;
+            if ((input = fopen(Catenate(path,"/",core,".fasta"),"r")) == NULL)
+              { free(core);
+                core = Root(ng->name,".fa");
+                if ((input = fopen(Catenate(path,"/",core,".fa"),"r")) == NULL)
+                  goto error;
+              }
             free(path);
           }
 

diff --git a/fasta2DB.c b/fasta2DB.c
@@ -371,8 +371,12 @@ int main(int argc, char *argv[])
 
             path  = PathTo(ng->name);
             core  = Root(ng->name,".fasta");
-            if ((input = Fopen(Catenate(path,"/",core,".fasta"),"r")) == NULL)
-              goto error;
+            if ((input = fopen(Catenate(path,"/",core,".fasta"),"r")) == NULL)
+              { free(core);
+                core = Root(ng->name,".fa");
+                if ((input = fopen(Catenate(path,"/",core,".fa"),"r")) == NULL)
+                  goto error;
+              }
             free(path);
           }