a few fixes, and a program to tabulate quality scores

diff --git a/configure.ac b/configure.ac
index 07fef16b40aa778437d01e1a3c7d85b79c91eec2..522949e39e50207dbb7df6d28724fd73796b6e24 100644 (file)
--- a/configure.ac
+++ b/configure.ac
@@ -8,8 +8,8 @@ AC_CONFIG_MACRO_DIR([m4])
 AC_PROG_CC
 AM_PROG_CC_C_O
 
-opt_CFLAGS="--std=c99 -Wall -g -O3"
-dbg_CFLAGS="--std=c99 -Wall -g -O0"
+opt_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O3"
+dbg_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O0"
 
 AC_ARG_ENABLE([debug],
               [AS_HELP_STRING([--enable-debug],

diff --git a/src/Makefile.am b/src/Makefile.am
index 989ae69c771ee501f1a2f040ae6c0190efb49b74..080e884de39ef1e55937c09d1522474cc9733568 100644 (file)
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,5 +1,5 @@
 
-bin_PROGRAMS = fastq-grep fastq-kmers fastq-match fastq-uniq
+bin_PROGRAMS = fastq-grep fastq-kmers fastq-match fastq-uniq fastq-qual
 
 fastq_common_src=common.h common.c
 fastq_parse_src=parse.h parse.c
@@ -18,4 +18,6 @@ fastq_match_LDADD   = -lz
 fastq_uniq_SOURCES = fastq-uniq.c $(fastq_common_src) $(fastq_parse_src) $(fastq_hash_src)
 fastq_uniq_LDADD   = -lz
 
+fastq_qual_SOURCES = fastq-qual.c $(fastq_common_src) $(fastq_parse_src) $(fastq_qual_src)
+fastq_qual_LDADD   = -lz
 

diff --git a/src/fastq-match.c b/src/fastq-match.c
index 53af1343c1756f5389dfa2ba18d1b6d9e615fb3a..bd040a6cf7df9535dc3bd1e1924f4d7157476d7a 100644 (file)
--- a/src/fastq-match.c
+++ b/src/fastq-match.c
@@ -43,9 +43,7 @@ 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;
 
@@ -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);
         }
     }
 

diff --git a/src/fastq-qual.c b/src/fastq-qual.c
new file mode 100644 (file)
index 0000000..5201376
--- /dev/null
+++ b/src/fastq-qual.c
@@ -0,0 +1,149 @@
+
+/*
+ * This file is part of fastq-tools.
+ *
+ * Copyright (c) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
+ *
+ * fastq-qual :
+ * Collect quality score statistics.
+ *
+ */
+
+#include "common.h"
+#include "parse.h"
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <getopt.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-qual [OPTION]... [FILE]...\n"
+"Output a tab-delimnated table such that row i, column j, given \n"
+"the number of times that quality score i occured in read position j\n\n."
+"Options:\n"
+"  -h, --help              print this message\n"
+"  -V, --version           output version information and exit\n");
+}
+
+
+
+void tally_quals(FILE* fin, unsigned int** xs, size_t* n)
+{
+    seq_t* seq = fastq_alloc_seq();
+    fastq_t* fqf = fastq_open(fin);
+
+    size_t i;
+
+    while (fastq_next(fqf, seq)) {
+        if (seq->qual.n > *n) {
+            *xs = realloc_or_die(*xs, 255 * seq->qual.n * sizeof(unsigned int));
+            memset(*xs + *n, 0, 255 * (seq->qual.n - *n) * sizeof(unsigned int));
+            *n  = seq->qual.n;
+        }
+
+
+        for (i = 0; i < seq->qual.n; ++i) {
+            (*xs)[i * 255 + (int) seq->qual.s[i]] += 1;
+        }
+    }
+
+    fastq_free_seq(seq);
+    fastq_close(fqf);
+}
+
+
+
+
+void print_table(FILE* fout, unsigned int* xs, size_t n)
+{
+    size_t i, j;
+
+    for (j = 0; j < 255; ++j) {
+        fprintf(fout, "%u", xs[j]);
+        for (i = 1; i < n; ++i) {
+            fprintf(fout, "\t%u", xs[i * 255 + j]);
+        }
+        fputc('\n', fout);
+    }
+}
+
+
+
+int main(int argc, char* argv[])
+{
+    SET_BINARY_MODE(stdin);
+    SET_BINARY_MODE(stdout);
+
+    FILE* fin;
+
+    int opt;
+    int opt_idx;
+    static struct option long_options[] =
+        { 
+          {"help",    no_argument,    0, 'h'},
+          {"version", no_argument, 0, 'V'},
+          {0, 0, 0, 0}
+        };
+
+    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();
+        }
+    }
+
+
+    size_t n = 0;
+    unsigned int* xs = NULL;
+
+    if (optind >= argc || (argc - optind == 1 && strcmp(argv[optind],"-") == 0)) {
+        tally_quals(stdin, &xs, &n);
+    }
+    else {
+        for (; optind < argc; optind++) {
+            fin = fopen(argv[optind], "rb");
+            if (fin == NULL) {
+                fprintf(stderr, "No such file '%s'.\n", argv[optind]);
+                continue;
+            }
+
+            tally_quals(fin, &xs, &n);
+        }
+    }
+
+    print_table(stdout, xs, n);
+
+    free(xs);
+
+    return 0;
+}
+
+

diff --git a/src/fastq-uniq.c b/src/fastq-uniq.c
index 32d344e29e1abfd10fa44203b1d94c1861fd8974..2e507622ddb38ebb0bcc97bd9b9a7c403d9ddf2e 100644 (file)
--- a/src/fastq-uniq.c
+++ b/src/fastq-uniq.c
@@ -13,6 +13,7 @@
 #include "hash.h"
 #include "parse.h"
 #include <string.h>
+#include <inttypes.h>
 #include <zlib.h>
 #include <getopt.h>
 
@@ -84,7 +85,7 @@ void print_hash_table(FILE* fout, hash_table* T)
 
     size_t i;
     for (i = 0; i < T->m; i++) {
-        fprintf(fout, ">unique-read-%07zu (%zu copies)\n", i, S[i]->count);
+        fprintf(fout, ">unique-read-%07zu (%"PRIu32" copies)\n", i, S[i]->count);
         fwrite(S[i]->value, S[i]->len, sizeof(char), fout);
         fprintf(fout, "\n");
     }

diff --git a/src/parse.c b/src/parse.c
index 9a7774d381a982972a67e4c806ebb46b7066a7d1..1ccc7de241306890665c413a1ab34e64c568b37d 100644 (file)
--- a/src/parse.c
+++ b/src/parse.c
@@ -67,7 +67,7 @@ typedef enum
 fastq_t* fastq_open(FILE* f)
 {
     fastq_t* fqf = malloc_or_die(sizeof(fastq_t));
-    or_die((int)(fqf->file = gzdopen(fileno(f), "rb")),
+    or_die((int)((fqf->file = gzdopen(fileno(f), "rb")) != NULL),
            "Can not open gzip file.");
     
     fqf->state = STATE_ID1;
@@ -113,7 +113,7 @@ void fastq_refill(fastq_t* f)
 
 void fastq_get_line(fastq_t* f, str_t* s)
 {
-    int i = 0;
+    size_t i = 0;
 
     if (f->state == STATE_EOF) goto fastq_get_line_done;
 
@@ -169,10 +169,12 @@ int fastq_next(fastq_t* f, seq_t* seq)
         }
 
         /* skip comments */
+        /*
         else if (*f->c == ';') {
             fastq_get_line(f, NULL);
             if (f->state == STATE_EOF) return 0;
         }
+        */
 
         /* read id1 */
         else if (f->state == STATE_ID1) {