a program to output a nonredundant list of readss

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

diff --git a/src/fastq-grep.c b/src/fastq-grep.c
index 08402b40b5876f086badb53373fe5c9dcd9d3b22..67c91901ead7d4a8320605c06ef4d72013966186 100644 (file)
--- a/src/fastq-grep.c
+++ b/src/fastq-grep.c
@@ -1,51 +1,126 @@
 
-
-/* 
- * fastq-grep: regular expression searches of the sequences within a fastq file
+/*
+ * This file is part of fastq-tools.
+ *
+ * Copyright (c) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
  *
- * Febuary 2011 / Daniel Jones <dcjones@cs.washington.edu> 
+ * fastq-grep :
+ * Regular expression searches of the sequences within a FASTQ file.
  *
  */
 
 
+#include "common.h"
+#include "parse.h"
 #include <stdio.h>
 #include <string.h>
 #include <getopt.h>
 #include <zlib.h>
 #include <pcre.h>
 
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
+
+#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
 
 
 void print_help()
 {
     fprintf( stderr, 
 "fastq-grep [OPTION]... PATTERN [FILE]...\n"
-"Search for PATTERN in the read sequence in each FILE or standard input.\n"
-"PATTERN, by default, is a perl compatible regular expression."
+"Search for PATTERN in the read sequences in each FILE or standard input.\n"
+"PATTERN, by default, is a perl compatible regular expression.\n\n"
+"Options:\n"
+"  -h, --help              print this message\n"
+"  -v, --invert-match      select nonmatching entries\n"
+"  -c, --count             output only the number of matching sequences\n"
     );
-
 }
 
 static int invert_flag;
 static int help_flag;
+static int count_flag;
+
+
+
+void print_fastq_entry(FILE* fout, seq_t* seq)
+{
+    fprintf(fout, "@%s\n%s\n+%s\n%s\n",
+                  seq->id1.s,
+                  seq->seq.s,
+                  seq->id2.s,
+                  seq->qual.s );
+}
+
+
+void fastq_grep(FILE* fin, FILE* fout, pcre* re)
+{
+    int rc;
+    int ovector[3];
+    size_t count = 0;
+
+    fastq_t* fqf = fastq_open(fin);
+    seq_t* seq = fastq_alloc_seq();
+
+    while (fastq_next(fqf, seq)) {
+        rc = pcre_exec(re,          /* pattern */
+                       NULL,        /* extre data */
+                       seq->seq.s,  /* subject */
+                       seq->seq.n,  /* subject length */
+                       0,           /* subject offset */
+                       0,           /* options */
+                       ovector,     /* output vector */
+                       3         ); /* output vector length */
+
+        if ((invert_flag && rc == PCRE_ERROR_NOMATCH) || rc >= 0) {
+            if (count_flag) count++;
+            else            print_fastq_entry(fout, seq);
+        }
+    }
+
+    fastq_free_seq(seq);
+    fastq_close(fqf);
+
+    if (count_flag) fprintf(fout, "%zu\n", count);
+}
+
+
 
 int main(int argc, char* argv[])
 {
+    SET_BINARY_MODE(stdin);
+    SET_BINARY_MODE(stdout);
+
+    const char* pat;
+    pcre* re;
+    const char* pat_error;
+    int pat_error_offset;
+
+    FILE*  fin;
+
+
+    invert_flag  = 0;
+    help_flag    = 0;
+    count_flag   = 0;
 
     int opt;
     int opt_idx;
 
+
     static struct option long_options[] =
         { 
           {"help", no_argument, &help_flag, 1},
           {"invert-match", no_argument, &invert_flag, 1},
+          {"count", no_argument, &count_flag, 1},
           {0, 0, 0, 0}
         };
 
     while (1) {
-        opt = getopt_long(argc, argv, "hv", long_options, &opt_idx);
+        opt = getopt_long(argc, argv, "hvc", long_options, &opt_idx);
 
         if( opt == -1 ) break;
 
@@ -53,7 +128,6 @@ int main(int argc, char* argv[])
             case 0:
                 if (long_options[opt_idx].flag != 0) break;
                 if (optarg) {
-                    /* TODO */
                 }
                 break;
 
@@ -65,6 +139,13 @@ int main(int argc, char* argv[])
                 invert_flag = 1;
                 break;
 
+            case 'c':
+                count_flag = 1;
+                break;
+
+            case '?':
+                return 1;
+
             default:
                 abort();
         }
@@ -75,7 +156,40 @@ int main(int argc, char* argv[])
         return 0;
     }
 
-    /* TODO */
+    if (optind >= argc) {
+        fprintf(stderr, "A pattern must be specified.\n");
+        return 1;
+    }
+
+    pat = argv[optind++];
+    re = pcre_compile( pat, PCRE_CASELESS, &pat_error, &pat_error_offset, NULL );
+
+
+    if (re == NULL) {
+        fprintf(stderr, "Syntax error in PCRE pattern at offset: %d: %s\n",
+                pat_error_offset, pat_error );
+        return 1;
+    }
+
+
+    if (optind >= argc || (argc - optind == 1 && strcmp(argv[optind],"-") == 0)) {
+        fastq_grep(stdin, stdout, re);
+    }
+    else {
+        for (; optind < argc; optind++) {
+            fin = fopen(argv[optind], "rb");
+            if (fin == NULL) {
+                fprintf(stderr, "No such file '%s'.\n", argv[optind]);
+                continue;
+            }
+
+            fastq_grep(fin, stdout, re);
+
+            fclose(fin);
+        }
+    }
+
+    pcre_free(re);
 
     return 0;
 }