Fix the weird output behavior of fastq-sample.

diff --git a/configure.ac b/configure.ac
index 4e6c266dd21ae4169e47556141fc5109ea5b33f8..93e89b0b13cfeb02fd864bb74996a3331cded482 100644 (file)
--- a/configure.ac
+++ b/configure.ac
@@ -8,6 +8,14 @@ AC_CONFIG_MACRO_DIR([m4])
 AC_PROG_CC
 AM_PROG_CC_C_O
 
 AC_PROG_CC
 AM_PROG_CC_C_O
 

+m4_ifdef([AC_TYPE_UINT8_T],  [AC_TYPE_UINT8_T])
+m4_ifdef([AC_TYPE_UINT16_T], [AC_TYPE_UINT16_T])
+m4_ifdef([AC_TYPE_INT32_T],  [AC_TYPE_INT32_T])
+m4_ifdef([AC_TYPE_UINT32_T], [AC_TYPE_UINT32_T])
+m4_ifdef([AC_TYPE_UINT64_T], [AC_TYPE_UINT64_T])
+m4_ifdef([AC_TYPE_SIZE_T],   [AC_TYPE_SIZE_T])
+m4_ifdef([AC_HEADER_STDBOOL], [AC_HEADER_STDBOOL])
+

 opt_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O3"
 dbg_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O0"
 
 opt_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O3"
 dbg_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O0"
 

diff --git a/doc/fastq-sample.1 b/doc/fastq-sample.1
index 4ce0cb4e6b87c2d20d7c7c0a2385a9fbafdc3b85..0ec7d7273e4c9fb420282c6515a0c73fe9a3eabe 100644 (file)
--- a/doc/fastq-sample.1
+++ b/doc/fastq-sample.1
@@ -28,7 +28,7 @@ sampling with replacement, this number may be greater than 1.0.
 \fB\-o\fR, \fB\-\-output=PREFIX\fR
 The filename prefix to which output should be written. If single-end data is
 being sampled, the output file is [PREFIX].fastq, and with paired-end,
 \fB\-o\fR, \fB\-\-output=PREFIX\fR
 The filename prefix to which output should be written. If single-end data is
 being sampled, the output file is [PREFIX].fastq, and with paired-end,

-[PREFIX].1.fastq and [PREFIX].2.fastq.
+[PREFIX].1.fastq and [PREFIX].2.fastq. (Default: \"sample\")

 .TP
 \fB\-r\fR, \fB\-\-with\-replacement\fR
 Sample with replacement. (By default, sampling is done without replacement.)
 .TP
 \fB\-r\fR, \fB\-\-with\-replacement\fR
 Sample with replacement. (By default, sampling is done without replacement.)

diff --git a/m4/ax_check_zlib.m4 b/m4/ax_check_zlib.m4
deleted file mode 100644 (file)
index d308183..0000000
--- a/m4/ax_check_zlib.m4
+++ /dev/null
@@ -1,133 +0,0 @@
-# ===========================================================================
-#       http://www.gnu.org/software/autoconf-archive/ax_check_zlib.html
-# ===========================================================================
-#
-# SYNOPSIS
-#
-#   AX_CHECK_ZLIB()
-#
-# DESCRIPTION
-#
-#   This macro searches for an installed zlib library. If nothing was
-#   specified when calling configure, it searches first in /usr/local and
-#   then in /usr, /opt/local and /sw. If the --with-zlib=DIR is specified,
-#   it will try to find it in DIR/include/zlib.h and DIR/lib/libz.a. If
-#   --without-zlib is specified, the library is not searched at all.
-#
-#   If either the header file (zlib.h) or the library (libz) is not found,
-#   the configuration exits on error, asking for a valid zlib installation
-#   directory or --without-zlib.
-#
-#   The macro defines the symbol HAVE_LIBZ if the library is found. You
-#   should use autoheader to include a definition for this symbol in a
-#   config.h file. Sample usage in a C/C++ source is as follows:
-#
-#     #ifdef HAVE_LIBZ
-#     #include <zlib.h>
-#     #endif /* HAVE_LIBZ */
-#
-# LICENSE
-#
-#   Copyright (c) 2008 Loic Dachary <loic@senga.org>
-#   Copyright (c) 2010 Bastien Chevreux <bach@chevreux.org>
-#
-#   This program is free software; you can redistribute it and/or modify it
-#   under the terms of the GNU General Public License as published by the
-#   Free Software Foundation; either version 2 of the License, or (at your
-#   option) any later version.
-#
-#   This program is distributed in the hope that it will be useful, but
-#   WITHOUT ANY WARRANTY; without even the implied warranty of
-#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
-#   Public License for more details.
-#
-#   You should have received a copy of the GNU General Public License along
-#   with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-#   As a special exception, the respective Autoconf Macro's copyright owner
-#   gives unlimited permission to copy, distribute and modify the configure
-#   scripts that are the output of Autoconf when processing the Macro. You
-#   need not follow the terms of the GNU General Public License when using
-#   or distributing such scripts, even though portions of the text of the
-#   Macro appear in them. The GNU General Public License (GPL) does govern
-#   all other use of the material that constitutes the Autoconf Macro.
-#
-#   This special exception to the GPL applies to versions of the Autoconf
-#   Macro released by the Autoconf Archive. When you make and distribute a
-#   modified version of the Autoconf Macro, you may extend this special
-#   exception to the GPL to apply to your modified version as well.
-
-#serial 8
-
-AU_ALIAS([CHECK_ZLIB], [AX_CHECK_ZLIB])
-AC_DEFUN([AX_CHECK_ZLIB],
-#
-# Handle user hints
-#
-[AC_MSG_CHECKING(if zlib is wanted)
-AC_ARG_WITH(zlib,
-[  --with-zlib=DIR root directory path of zlib installation [defaults to
-                    /usr/local or /usr if not found in /usr/local]
-  --without-zlib to disable zlib usage completely],
-[if test "$withval" != no ; then
-  zlib_places="/usr/local /usr /opt/local /sw"
-  AC_MSG_RESULT(yes)
-  if test -d "$withval"
-  then
-    zlib_places="$withval $zlib_places"
-  else
-    AC_MSG_WARN([Sorry, $withval does not exist, checking usual places])
-  fi
-else
-  AC_MSG_RESULT(no)
-fi],
-[AC_MSG_RESULT(yes)])
-
-#
-# Locate zlib, if wanted
-#
-if test -n "${zlib_places}"
-then
-       # check the user supplied or any other more or less 'standard' place:
-       #   Most UNIX systems      : /usr/local and /usr
-       #   MacPorts / Fink on OSX : /opt/local respectively /sw
-       for ZLIB_HOME in ${zlib_places} ; do
-         if test -f "${ZLIB_HOME}/include/zlib.h"; then break; fi
-         ZLIB_HOME=""
-       done
-
-       # if zlib.h was nowhere to be found, give a notice and bail out
-       if test ! -n "${ZLIB_HOME}"; then
-          AC_MSG_ERROR(No zlib.h in any include directory of ${zlib_places}: either specify a valid zlib installation with --with-zlib=DIR or disable zlib usage with --without-zlib)
-       fi
-
-        ZLIB_OLD_LDFLAGS=$LDFLAGS
-        ZLIB_OLD_CPPFLAGS=$LDFLAGS
-        LDFLAGS="$LDFLAGS -L${ZLIB_HOME}/lib"
-        CPPFLAGS="$CPPFLAGS -I${ZLIB_HOME}/include"
-        AC_LANG_SAVE
-        AC_LANG_C
-        AC_CHECK_LIB(z, inflateEnd, [zlib_cv_libz=yes], [zlib_cv_libz=no])
-        AC_CHECK_HEADER(zlib.h, [zlib_cv_zlib_h=yes], [zlib_cv_zlib_h=no])
-        AC_LANG_RESTORE
-        if test "$zlib_cv_libz" = "yes" -a "$zlib_cv_zlib_h" = "yes"
-        then
-                #
-                # If both library and header were found, use them
-                #
-                AC_CHECK_LIB(z, inflateEnd)
-                AC_MSG_CHECKING(zlib in ${ZLIB_HOME})
-                AC_MSG_RESULT(ok)
-        else
-                #
-                # If either header or library was not found, revert and bomb
-                #
-                AC_MSG_CHECKING(zlib in ${ZLIB_HOME})
-                LDFLAGS="$ZLIB_OLD_LDFLAGS"
-                CPPFLAGS="$ZLIB_OLD_CPPFLAGS"
-                AC_MSG_RESULT(failed)
-                AC_MSG_ERROR(either specify a valid zlib installation with --with-zlib=DIR or disable zlib usage with --without-zlib)
-        fi
-fi
-
-])

diff --git a/src/Makefile.am b/src/Makefile.am
index 84707f23fe3f31e564e56fc81f943deb8ab876e8..aeb9c85f6a2df5288462021a6613c246b65b6f0d 100644 (file)
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -8,22 +8,16 @@ fastq_hash_src=hash.h hash.c
 fastq_rng_src=rng.h rng.c
 
 fastq_grep_SOURCES = fastq-grep.c $(fastq_common_src) $(fastq_parse_src)
 fastq_rng_src=rng.h rng.c
 
 fastq_grep_SOURCES = fastq-grep.c $(fastq_common_src) $(fastq_parse_src)

-fastq_grep_LDADD = $(PCRE_LIBS) -lz
+fastq_grep_LDADD = $(PCRE_LIBS)

 
 fastq_kmers_SOURCES = fastq-kmers.c $(fastq_common_src) $(fastq_parse_src)
 
 fastq_kmers_SOURCES = fastq-kmers.c $(fastq_common_src) $(fastq_parse_src)

-fastq_kmers_LDADD = -lz

 
 fastq_match_SOURCES = fastq-match.c $(fastq_common_src) $(fastq_parse_src) $(fastq_sw_src)
 
 fastq_match_SOURCES = fastq-match.c $(fastq_common_src) $(fastq_parse_src) $(fastq_sw_src)

-fastq_match_LDADD   = -lz

 
 fastq_uniq_SOURCES = fastq-uniq.c $(fastq_common_src) $(fastq_parse_src) $(fastq_hash_src)
 
 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_SOURCES = fastq-qual.c $(fastq_common_src) $(fastq_parse_src)

-fastq_qual_LDADD   = -lz

 
 fastq_sample_SOURCES = fastq-sample.c $(fastq_common_src) $(fastq_parse_src) $(fastq_rng_src)
 
 fastq_sample_SOURCES = fastq-sample.c $(fastq_common_src) $(fastq_parse_src) $(fastq_rng_src)

-fastq_sample_LDADD   = -lz

 
 fastq_qualadj_SOURCES = fastq-qualadj.c $(fastq_common_src) $(fastq_parse_src)
 
 fastq_qualadj_SOURCES = fastq-qualadj.c $(fastq_common_src) $(fastq_parse_src)

-fastq_qualadj_LDADD   = -lz

diff --git a/src/common.c b/src/common.c
index b3f47edc166e5a2027cd6f3cb34cc2e04e2830d9..9a11aecf47bf1cb59331da7a8da42a02242b3f5f 100644 (file)
--- a/src/common.c
+++ b/src/common.c
@@ -6,10 +6,16 @@
  *
  */
 
  *
  */
 

+#include <errno.h>
+#include <fcntl.h>
+#include <stdlib.h>

 
 #include "common.h"
 #include "version.h"
 
 #include "common.h"
 #include "version.h"

-#include <stdlib.h>
+
+#ifndef O_BINARY
+#define O_BINARY 0
+#endif

 
 
 void print_version(FILE *f, const char* prog_name)
 
 
 void print_version(FILE *f, const char* prog_name)


@@ -61,4 +67,31 @@ FILE* fopen_or_die(const char* path, const char* mode)
 }
 
 
 }
 
 

+/* Open a file for writing, creating it if it doesn't exist, and complaining if
+ * it does. */
+FILE* open_without_clobber(const char* filename)
+{
+    int fd = open(filename, O_WRONLY | O_CREAT | O_BINARY | O_EXCL,
+                  S_IRUSR | S_IWUSR);
+
+    if (fd == -1) {
+        if (errno == EEXIST) {
+            fprintf(stderr, "Refusing to overwrite %s.\n", filename);
+            exit(EXIT_FAILURE);
+        }
+        else {
+            fprintf(stderr, "Cannot open %s for writing.\n", filename);
+            exit(EXIT_FAILURE);
+        }
+    }
+
+    FILE* f = fdopen(fd, "wb");
+    if (f == NULL) {
+        fprintf(stderr, "Cannot open %s for writing.\n", filename);
+        exit(EXIT_FAILURE);
+    }
+
+    return f;
+}
+

 
 

diff --git a/src/common.h b/src/common.h
index 163755bd925d09b2aa4986ef27fd9dd6f80e10f7..5cc34fba0ca115f77c2f636594e2672f2501f579 100644 (file)
--- a/src/common.h
+++ b/src/common.h
@@ -21,5 +21,9 @@ void* malloc_or_die(size_t);
 void* realloc_or_die(void*, size_t);
 FILE* fopen_or_die(const char*, const char*);
 
 void* realloc_or_die(void*, size_t);
 FILE* fopen_or_die(const char*, const char*);
 

+/* Open a file for reading, creating it if it doesn't exist, and complaining if
+ * it does. */
+FILE* open_without_clobber(const char* filename);
+

 #endif
 
 #endif
 

diff --git a/src/fastq-sample.c b/src/fastq-sample.c
index d3c2b550e3c128844d7df678764242a3d49c1be6..0adf02dd27c6d6d73c3c1ae08ddd36ec4729084b 100644 (file)
--- a/src/fastq-sample.c
+++ b/src/fastq-sample.c
@@ -8,23 +8,16 @@
  * Sample reads with or without replacement from a FASTQ file.
  *
  */
  * Sample reads with or without replacement from a FASTQ file.
  *
  */

+#include <getopt.h>
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>

 
 #include "common.h"
 #include "parse.h"
 #include "rng.h"
 
 #include "common.h"
 #include "parse.h"
 #include "rng.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-sample";
 
 
 static const char* prog_name = "fastq-sample";
 


@@ -39,7 +32,7 @@ void print_help()
 "Options:\n"
 "  -n N                    the number of reads to sample (default: 10000)\n"
 "  -p N                    the proportion of the total reads to sample\n"
 "Options:\n"
 "  -n N                    the number of reads to sample (default: 10000)\n"
 "  -p N                    the proportion of the total reads to sample\n"

-"  -o, --output=PREFIX     output file prefix\n"
+"  -o, --output=PREFIX     output file prefix\n (Default: \"sample\")"

 "  -c, --complement-output=PREFIX\n"
 "                          output reads not included in the random sample to\n"
 "                          a file (or files) with the given prefix (by default,\n"
 "  -c, --complement-output=PREFIX\n"
 "                          output reads not included in the random sample to\n"
 "                          a file (or files) with the given prefix (by default,\n"


@@ -48,7 +41,7 @@ void print_help()
 "  -s, --seed=SEED         a manual seed to the random number generator\n"
 "  -h, --help              print this message\n"
 "  -V, --version           output version information and exit\n"
 "  -s, --seed=SEED         a manual seed to the random number generator\n"
 "  -h, --help              print this message\n"
 "  -V, --version           output version information and exit\n"

-    );
+);

 }
 
 
 }
 
 


@@ -103,25 +96,25 @@ unsigned long* index_without_replacement(rng_t* rng, unsigned long n)
 
 
 void fastq_sample(unsigned long rng_seed,
 
 
 void fastq_sample(unsigned long rng_seed,

-                  const char* prefix, const char* cprefix,
-                  FILE* file1, FILE* file2, unsigned long k, double p)
+        const char* prefix, const char* cprefix,
+        FILE* file1, FILE* file2, unsigned long k, double p)

 {
 {

-     /*
-      * The basic idea is this:
-      *
-      * 1. Count the number of lines in the file, n.
-      *
-      * 2a. If sampling with replacement, generate k random integers in [0, n-1].
-      *
-      * 2b. If sampling without replacement, generate a list of integers 0..(n-1),
-      *     shuffle with fisher-yates, then consider the first k.
-      *
-      * 3. Sort the integer list.
-      *
-      * 3. Read through the file again, when the number at the front of the integer
-      *    list matches the index of the fastq etry, print the entry, and pop the
-      *    number.
-      */
+    /*
+     * The basic idea is this:
+     *
+     * 1. Count the number of lines in the file, n.
+     *
+     * 2a. If sampling with replacement, generate k random integers in [0, n-1].
+     *
+     * 2b. If sampling without replacement, generate a list of integers 0..(n-1),
+     *     shuffle with fisher-yates, then consider the first k.
+     *
+     * 3. Sort the integer list.
+     *
+     * 3. Read through the file again, when the number at the front of the integer
+     *    list matches the index of the fastq etry, print the entry, and pop the
+     *    number.
+     */

 
 
     unsigned long n, n2;
 
 
     unsigned long n, n2;


@@ -142,7 +135,7 @@ void fastq_sample(unsigned long rng_seed,
     if (f2 != NULL) fastq_rewind(f2);
 
     if (p > 0.0) {
     if (f2 != NULL) fastq_rewind(f2);
 
     if (p > 0.0) {

-        k = (unsigned long) (p * (double) n);
+        k = (unsigned long) round(p * (double) n);

         if (!replacement_flag && k > n) k = n;
     }
 
         if (!replacement_flag && k > n) k = n;
     }
 


@@ -155,7 +148,6 @@ void fastq_sample(unsigned long rng_seed,
 
     qsort(xs, k, sizeof(unsigned long), cmpul);
 
 
     qsort(xs, k, sizeof(unsigned long), cmpul);
 

-

     /* open output */
     FILE* fout1;
     FILE* fout2;
     /* open output */
     FILE* fout1;
     FILE* fout2;


@@ -167,7 +159,7 @@ void fastq_sample(unsigned long rng_seed,
         output_name = malloc_or_die((output_len + 1) * sizeof(char));
 
         snprintf(output_name, output_len, "%s.fastq", prefix);
         output_name = malloc_or_die((output_len + 1) * sizeof(char));
 
         snprintf(output_name, output_len, "%s.fastq", prefix);

-        fout1 = fopen(output_name, "wb");
+        fout1 = open_without_clobber(output_name);

         if (fout1 == NULL) {
             fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
             exit(1);
         if (fout1 == NULL) {
             fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
             exit(1);


@@ -182,14 +174,14 @@ void fastq_sample(unsigned long rng_seed,
         output_name = malloc_or_die((output_len + 1) * sizeof(char));
 
         snprintf(output_name, output_len, "%s.1.fastq", prefix);
         output_name = malloc_or_die((output_len + 1) * sizeof(char));
 
         snprintf(output_name, output_len, "%s.1.fastq", prefix);

-        fout1 = fopen(output_name, "wb");
+        fout1 = open_without_clobber(output_name);

         if (fout1 == NULL) {
             fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
             exit(1);
         }
 
         snprintf(output_name, output_len, "%s.2.fastq", prefix);
         if (fout1 == NULL) {
             fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
             exit(1);
         }
 
         snprintf(output_name, output_len, "%s.2.fastq", prefix);

-        fout2 = fopen(output_name, "wb");
+        fout1 = open_without_clobber(output_name);

         if (fout1 == NULL) {
             fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
             exit(1);
         if (fout1 == NULL) {
             fprintf(stderr, "Cannot open file %s for writing.\n", output_name);
             exit(1);


@@ -198,7 +190,6 @@ void fastq_sample(unsigned long rng_seed,
         free(output_name);
     }
 
         free(output_name);
     }
 

-

     /* open complement output */
     FILE* cfout1 = NULL;
     FILE* cfout2 = NULL;
     /* open complement output */
     FILE* cfout1 = NULL;
     FILE* cfout2 = NULL;


@@ -239,8 +230,6 @@ void fastq_sample(unsigned long rng_seed,
         free(output_name);
     }
 
         free(output_name);
     }
 

-
-

     unsigned long i = 0; // read number
     unsigned long j = 0; // index into xs
 
     unsigned long i = 0; // read number
     unsigned long j = 0; // index into xs
 


@@ -290,21 +279,17 @@ void fastq_sample(unsigned long rng_seed,
 
 int main(int argc, char* argv[])
 {
 
 int main(int argc, char* argv[])
 {

-    SET_BINARY_MODE(stdin);
-    SET_BINARY_MODE(stdout);
-

     int opt;
     int opt_idx;
 
     int opt;
     int opt_idx;
 

-    const char* prefix = NULL;
-    const char* cprefix = NULL;
+    const char* prefix = "sample";
+    const char* cprefix = NULL; 

     unsigned long rng_seed = 4357;
     unsigned long k = 10000; // number of reads to sample
     double        p = -1;    // proportion of reads to sample
 
     unsigned long rng_seed = 4357;
     unsigned long k = 10000; // number of reads to sample
     double        p = -1;    // proportion of reads to sample
 

-

     static struct option long_options[] =
     static struct option long_options[] =

-        { 
+        {

           {"with-replacement",  no_argument,       NULL, 'r'},
           {"complement-output", required_argument, NULL, 'c'},
           {"seed",              required_argument, NULL, 's'},
           {"with-replacement",  no_argument,       NULL, 'r'},
           {"complement-output", required_argument, NULL, 'c'},
           {"seed",              required_argument, NULL, 's'},


@@ -375,60 +360,28 @@ int main(int argc, char* argv[])
     FILE* file1 = NULL;
     FILE* file2 = NULL;
 
     FILE* file1 = NULL;
     FILE* file2 = NULL;
 

-    char* prefix_alloc = NULL;
-

     if (optind >= argc) {
         fputs("An input file must be given.\n", stderr);
         print_help();
     if (optind >= argc) {
         fputs("An input file must be given.\n", stderr);
         print_help();

-        exit(1);
+        return EXIT_FAILURE;

     }
     }

-    else {
-        file1 = fopen(argv[optind], "rb");
-        if (file1 == NULL) {
-            fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
-            return 1;
-        }

 
 

-        if (prefix == NULL) {
-            /* guess at a reasonable output refix by trimming the
-             * trailing file extension, if any.  */
-            char* tmp;
-
-            /* base name */
-            tmp = strrchr(argv[optind], '/');
-            if (tmp != NULL) argv[optind] = tmp + 1;
-
-            /* exclude file suffixes */
-            tmp = strchr(argv[optind], '.');
-            if (tmp == NULL) prefix = argv[optind];
-            else {
-                prefix_alloc = malloc_or_die((tmp - argv[optind] + 1) * sizeof(char));
-                memcpy(prefix_alloc, argv[optind], (tmp - argv[optind]) * sizeof(char));
-                prefix_alloc[tmp - argv[optind]] = '\0';
-                prefix = prefix_alloc;
-            }
-        }
-        ++optind;
+    file1 = fopen(argv[optind], "rb");
+    if (file1 == NULL) {
+        fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
+        return 1;
+    }

 
 

-        if (optind < argc) {
-            file2 = fopen(argv[optind], "rb");
-            if (file2 == NULL) {
-                fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
-                return 1;
-            }
+    if (++optind < argc) {
+        file2 = fopen(argv[optind], "rb");
+        if (file2 == NULL) {
+            fprintf(stderr, "Cannot open '%s' for reading.\n", argv[optind]);
+            return 1;

         }
     }
 
     fastq_sample(rng_seed, prefix, cprefix, file1, file2, k, p);
 
         }
     }
 
     fastq_sample(rng_seed, prefix, cprefix, file1, file2, k, p);
 

-    free(prefix_alloc);
-    return 0;
+    return EXIT_SUCCESS;

 }
 
 }
 

-
-
-
-
-
-
-

diff --git a/src/parse.c b/src/parse.c
index e27a3859ebdb24a6a9b7406fa0f9218d64b40e99..8a6123e9b97f14e6818421e8d2a9f06303fad78c 100644 (file)
--- a/src/parse.c
+++ b/src/parse.c
@@ -166,6 +166,14 @@ bool fastq_read(fastq_t* f, seq_t* seq)
 }
 
 
 }
 
 

+void fastq_rewind(fastq_t* f)
+{
+    rewind(f->file);
+    f->next = f->buf;
+    f->readlen = 0;
+}
+
+

 void fastq_print(FILE* fout, const seq_t* seq)
 {
     fprintf(fout, "@%s\n%s\n+%s\n%s\n",
 void fastq_print(FILE* fout, const seq_t* seq)
 {
     fprintf(fout, "@%s\n%s\n+%s\n%s\n",

diff --git a/src/parse.h b/src/parse.h
index 8500f0c832fc1fb6c7460afdaa0d7ee05ce4d891..6224ab8d07368e735cfcb7d504ea67da05994b6e 100644 (file)
--- a/src/parse.h
+++ b/src/parse.h
@@ -69,6 +69,13 @@ void fastq_free(fastq_t*);
 bool fastq_read(fastq_t* f, seq_t* seq);
 
 
 bool fastq_read(fastq_t* f, seq_t* seq);
 
 

+/* Rewind the fastq file.
+ *
+ * The FILE passed to fastq_create must be seekable for this to work.
+ */
+void fastq_rewind(fastq_t* f);
+
+

 /* Print a fastq entry. */
 void fastq_print(FILE* fout, const seq_t* seq);
 
 /* Print a fastq entry. */
 void fastq_print(FILE* fout, const seq_t* seq);
 

diff --git a/src/rng.c b/src/rng.c
index b5036997e6844279b0f05e737e29af4222f66f05..ac375d0312489a6b07d7d0d2f54532c12b1fec66 100644 (file)
--- a/src/rng.c
+++ b/src/rng.c
@@ -41,7 +41,7 @@
    your work".
 
    Makoto Matsumoto has a web page with more information about the
    your work".
 
    Makoto Matsumoto has a web page with more information about the

-   generator, http://www.math.keio.ac.jp/~matumoto/emt.html. 
+   generator, http://www.math.keio.ac.jp/~matumoto/emt.html.

 
    The paper below has details of the algorithm.
 
 
    The paper below has details of the algorithm.