Added a program to adjust quality scores by a fixed offset.

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

diff --git a/src/fastq-qualadj.c b/src/fastq-qualadj.c
new file mode 100644 (file)
index 0000000..b14e8c9
--- /dev/null
+++ b/src/fastq-qualadj.c
@@ -0,0 +1,136 @@
+
+/*
+ * This file is part of fastq-tools.
+ *
+ * Copyright (c) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
+ *
+ * fastq-qualadj:
+ * Adjust quality scores by a given offset.
+ *
+ */
+
+
+#include "common.h"
+#include "parse.h"
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <getopt.h>
+#include <zlib.h>
+
+
+#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
+#  include <fcntl.h>
+#  include <io.h>
+#  define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
+#else
+#  define SET_BINARY_MODE(file)
+#endif
+
+
+static const char* prog_name = "fastq-grep";
+
+void print_help()
+{
+    fprintf(stdout, 
+"fastq-qualadj [OPTION]... OFFSET [FILE]...\n"
+"The given offset is added to each and every quality score, where\n"
+"the offset may be negative.\n"
+"Options:\n"
+"  -h, --help              print this message\n"
+"  -V, --version           output version information and exit\n"
+    );
+}
+
+void fastq_qualadj(FILE* fin, FILE* fout, int offset)
+{
+    fastq_t* fqf = fastq_open(fin);
+    seq_t* seq = fastq_alloc_seq();
+    size_t i;
+    int c;
+
+    while (fastq_next(fqf, seq)) {
+        for (i = 0; i < seq->qual.n; ++i) {
+            c = (int) seq->qual.s[i] - offset;
+            c = c < 0 ? 0 : (c > 126 ? 126: c);
+            seq->qual.s[i] = (char) c;
+        }
+
+        fastq_print(fout, seq);
+    }
+
+    fastq_free_seq(seq);
+    fastq_close(fqf);
+}
+
+
+int main(int argc, char* argv[])
+{
+    SET_BINARY_MODE(stdin);
+    SET_BINARY_MODE(stdout);
+
+    char offset = 0;
+
+    static struct option long_options[] =
+        { 
+          {"help",         no_argument, NULL, 'h'},
+          {"version",      no_argument, NULL, 'V'},
+          {0, 0, 0, 0}
+        };
+
+    int opt;
+    int opt_idx;
+
+    while (1) {
+        opt = getopt_long(argc, argv, "hV", long_options, &opt_idx);
+
+        if (opt == -1) break;
+
+        switch(opt) {
+            case 'h':
+                print_help();
+                return 0;
+
+            case 'V':
+                print_version(stdout, prog_name);
+                return 0;
+
+            case '?':
+                return 1;
+
+            default:
+                abort();
+        }
+    }
+
+    if (optind >= argc) {
+        fprintf(stderr, "An offset must be specified.\n");
+        return 1;
+    }
+
+    offset = atoi(argv[optind++]);
+
+
+    FILE* fin;
+
+    if (optind >= argc || (argc - optind == 1 && strcmp(argv[optind],"-") == 0)) {
+        fastq_qualadj(stdin, stdout, offset);
+    }
+    else {
+        for (; optind < argc; optind++) {
+            fin = fopen(argv[optind], "rb");
+            if (fin == NULL) {
+                fprintf(stderr, "No such file '%s'.\n", argv[optind]);
+                continue;
+            }
+
+            fastq_qualadj(fin, stdout, offset);
+
+            fclose(fin);
+        }
+    }
+
+    return 0;
+}
+
+