Much simpler faster code for parsing fastq files.

[fastq-tools.git] / src / fastq-match.c

diff --git a/src/fastq-match.c b/src/fastq-match.c
index 53af1343c1756f5389dfa2ba18d1b6d9e615fb3a..1e4d9c705344af121b645869edaba736b78736a8 100644 (file)
--- a/src/fastq-match.c
+++ b/src/fastq-match.c
@@ -43,16 +43,14 @@ void print_help()
 }
 
 
-void fastq_match(FILE* fin, FILE* fout,
-                 sw_t* sw,
-                 unsigned char* query, int n)
+void fastq_match(FILE* fin, FILE* fout, sw_t* sw)
 {
     int score;
 
-    fastq_t* fqf = fastq_open(fin);
-    seq_t* seq = fastq_alloc_seq();
+    fastq_t* fqf = fastq_create(fin);
+    seq_t* seq = seq_create();
 
-    while (fastq_next(fqf, seq)) {
+    while (fastq_read(fqf, seq)) {
         fprintf(fout, "%s\t", seq->seq.s);
 
         fastq_sw_conv_seq((unsigned char*)seq->seq.s, seq->seq.n);
@@ -61,8 +59,8 @@ void fastq_match(FILE* fin, FILE* fout,
         fprintf(fout, "%d\n", score);
     }
 
-    fastq_free_seq(seq);
-    fastq_close(fqf);
+    seq_free(seq);
+    fastq_free(fqf);
 }
 
 
@@ -131,7 +129,7 @@ int main(int argc, char* argv[])
     sw = fastq_alloc_sw(query, query_len);
 
     if (optind >= argc || (argc - optind == 1 && strcmp(argv[optind],"-") == 0)) {
-        fastq_match(stdin, stdout, sw, query, query_len);
+        fastq_match(stdin, stdout, sw);
     }
     else {
         for (; optind < argc; optind++) {
@@ -141,7 +139,7 @@ int main(int argc, char* argv[])
                 continue;
             }
 
-            fastq_match(fin, stdout, sw, query, query_len);
+            fastq_match(fin, stdout, sw);
         }
     }