fix: compile all

src/abi/makefile-alpha

@@ -5,7 +5,8 @@
 #
 # Programs made by this makefile
 #
-PROGS = getABISampleName
+PROGS = getABISampleName 2rs
+all: $(PROGS)
 
 #
 # Where the wild things are
@@ -26,6 +27,8 @@ LDFLAGS = -g
 getABISampleName: getABISampleName.o
 	$(LD) $(LDFLAGS) -o getABISampleName getABISampleName.o
 
+2rs: 2rs.o
+	$(LD) $(LDFLAGS) -o 2rs 2rs.o
 
 #
 # Special dependencies

src/cop/makefile-alpha

@@ -6,7 +6,7 @@
 # Programs made by this makefile
 #
 PROGS = cop cop-bap
-
+all: $(PROGS)
 #
 # Where the wild things are
 #

src/getMCH/makefile-alpha

@@ -23,7 +23,7 @@
 # Programs made by this makefile
 #
 PROGS = getMCH trace2seq
-
+all: $(PROGS)
 #
 # Where the wild things are
 #

src/indexseqlibs/excludewords.c

@@ -13,7 +13,7 @@ static FILE *out;
 
 static int line_comp(char *ex, char *in, int l)
 /*
-** Compare exclude line with inline
+** Compare exclude line with cinline
 */
 {
     return strncmp(ex,in+11,l);
@@ -28,13 +28,13 @@ static void process()
 */
 {
     char exline[MAXLINE];
-    char inline[MAXLINE];
+    char cinline[MAXLINE];
     char *exok, *inok;
     int compare;
 
 
     exok = fgets(exline,MAXLINE,ex);
-    inok = fgets(inline,MAXLINE,in);
+    inok = fgets(cinline,MAXLINE,in);
 
     while (exok && inok) {
 
@@ -43,15 +43,15 @@ static void process()
 	if (compare < 0)
 	    exok = fgets(exline,MAXLINE,ex);
 	else if (compare > 0) {
-	    fprintf(out,"%s",inline);
-	    inok = fgets(inline,MAXLINE,in);
+	    fprintf(out,"%s",cinline);
+	    inok = fgets(cinline,MAXLINE,in);
 	} else
-	    inok = fgets(inline,MAXLINE,in);
+	    inok = fgets(cinline,MAXLINE,in);
 
     }
 
-    while (inok = fgets(inline,MAXLINE,in))
-	fprintf(out,"%s",inline);
+    while (inok = fgets(cinline,MAXLINE,in))
+	fprintf(out,"%s",cinline);
 
 }
 

src/indexseqlibs/makefile-alpha

@@ -2,6 +2,7 @@
 # indexseqlibs - Alpha version
 #
 
+all: $(PROGS)
 
 #
 # Programs need making