add mer list reading to strstream

1 files changed, 71 insertions, 13 deletions

diff --git a/src/strstream.c b/src/strstream.c
index f4a296e..c4c30fa 100644
--- a/src/strstream.c
+++ b/src/strstream.c
@@ -4,11 +4,52 @@
 #include <string.h>
 #include <unistd.h>
 
+char **load_mers_from_file(FILE *fh, ssize_t *len) {
+	char line[4096];
+
+	size_t realloc_size = 1;
+	*len = 0;
+
+	char **mers = NULL;
+
+	while((fgets(line, 4096, fh)) != NULL) { 
+		size_t line_len = strlen(line);
+		if(line_len == 0) 
+			continue;
+
+		line[line_len - 1] = '\0';
+
+		mers = realloc(mers, sizeof(char *) * realloc_size);
+		if(mers == NULL) {
+			fprintf(stderr, "could not realloc mers\n");
+			exit(EXIT_FAILURE);
+		}
+
+		char *cpy = malloc(line_len + 1);
+		if(cpy == NULL) {
+			fprintf(stderr, "could not alloc mers\n");
+			exit(EXIT_FAILURE);
+		}
+		strncpy(cpy, line, line_len);
+		mers[*len] = cpy;
+		*len += 1;
+
+		realloc_size++;
+	}
+
+	if(*len != 0)
+		return mers;
+
+	*len = -1;
+	return NULL;
+}
+
 int main(int argc, char **argv){
 
 	char buffer[BUFSIZ] = { 0 };
 	char *buf, *start;
 	ssize_t len = 0;
+	ssize_t mer_len = 0;
 
 	int save_size = 0;
 	int cpy = 0;
@@ -18,11 +59,33 @@ int main(int argc, char **argv){
 
 	int i = 0;
 
+	if(argc != 3)  {
+		fprintf(stderr, "usage: strstream merlist.txt\n");
+		exit(EXIT_FAILURE);
+	}
+	//
+	FILE *infh = fopen(argv[2], "r");
+	if(infh == NULL) {
+		fprintf(stderr, "could not open %s\n", argv[2]);
+		exit(EXIT_FAILURE);
+	}
+	// load mers
+	FILE *fh = fopen(argv[1], "r");
+	if(fh == NULL) {
+		fprintf(stderr, "could not open %s\n", argv[1]);
+		exit(EXIT_FAILURE);
+	}
+	char **mers = load_mers_from_file(fh, &mer_len);
+	if(mers == NULL) {
+		fprintf(stderr, "could not load mers from %s\n", argv[1]);
+		exit(EXIT_FAILURE);
+	}
+
 	// get max argument length
-	for(i = 1; i < argc; i++) {
-		int len = strlen(argv[i]);
-		if(len > save_size)
-			save_size = len;
+	for(i = 0; i < mer_len; i++) {
+		int current_len = strlen(mers[i]);
+		if( current_len > save_size)
+			save_size = current_len;
 	}
 
 	cpy = save_size - 1;
@@ -31,17 +94,12 @@ int main(int argc, char **argv){
 	buf = buffer;
 	start = buf + cpy;
 
-	// copy our first cpy length into the first part of our buffer
-	len = fread(buffer, 1, cpy, stdin);
-	if(len == 0) 
-		exit(EXIT_FAILURE);
-
 	// read into "start" (buf + cpy) from stdin
-	while((len = fread(start, 1, cpy_size, stdin)) != 0) {
-		for(i = 1; i < argc; i++) {
+	while((len = fread(start, 1, cpy_size, infh)) != 0) {
+		for(i = 0; i < mer_len; i++) {
 			char *p = buffer;
-			while((p = strstr(p, argv[i])) != NULL) {
-				printf("%d %llu\n", i - 1, pos + (p - buffer));
+				while((p = strstr(p, mers[i])) != NULL) {
+				printf("%d %llu\n", i, pos + (p - buffer));
 				p++;
 			}
 		}