Much simpler faster code for parsing fastq files.

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

diff --git a/src/fastq-qualadj.c b/src/fastq-qualadj.c
index 60479c1c9dfb59712f47b9a09618a9f9c7593914..51919b0c52691dd1a2782e12989218d46b6ebcfc 100644 (file)
--- a/src/fastq-qualadj.c
+++ b/src/fastq-qualadj.c
@@ -44,14 +44,14 @@ void print_help()
 
 void fastq_qualadj(FILE* fin, FILE* fout, int offset)
 {
-    fastq_t* fqf = fastq_open(fin);
-    seq_t* seq = fastq_alloc_seq();
+    fastq_t* fqf = fastq_create(fin);
+    seq_t* seq = seq_create();
     size_t i;
     int c;
 
-    while (fastq_next(fqf, seq)) {
+    while (fastq_read(fqf, seq)) {
         for (i = 0; i < seq->qual.n; ++i) {
-            c = (int) seq->qual.s[i] - offset;
+            c = (int) seq->qual.s[i] + offset;
             c = c < 0 ? 0 : (c > 126 ? 126: c);
             seq->qual.s[i] = (char) c;
         }
@@ -59,8 +59,8 @@ void fastq_qualadj(FILE* fin, FILE* fout, int offset)
         fastq_print(fout, seq);
     }
 
-    fastq_free_seq(seq);
-    fastq_close(fqf);
+    seq_free(seq);
+    fastq_free(fqf);
 }
 
 
@@ -137,8 +137,6 @@ int main(int argc, char* argv[])
     }
     else if (offset == 0) offset = atoi(argv[optind++]);
 
-    fprintf(stderr, "%d\n", offset);
-
     FILE* fin;
 
     if (optind >= argc || (argc - optind == 1 && strcmp(argv[optind],"-") == 0)) {