diff options
| -rw-r--r-- | Makefile.osx | 43 | ||||
| -rw-r--r-- | getline/getdelim.c | 119 | ||||
| -rw-r--r-- | getline/getdelim.h | 28 | ||||
| -rw-r--r-- | getline/getline.c | 152 | ||||
| -rw-r--r-- | getline/getline.h | 53 | ||||
| -rw-r--r-- | kmer_counts_per_sequence.c | 4 | ||||
| -rw-r--r-- | kmer_locations.c | 4 | ||||
| -rw-r--r-- | kmer_total_count.c | 4 | ||||
| -rw-r--r-- | kmer_utils.c | 4 |
9 files changed, 409 insertions, 2 deletions
diff --git a/Makefile.osx b/Makefile.osx new file mode 100644 index 0000000..104512f --- /dev/null +++ b/Makefile.osx @@ -0,0 +1,43 @@ +VERSION=\"0.0.5\" +CC = x86_64-apple-darwin10-g++-mp-4.8 +CFLAGS = -O3 -s -march=native -Wall -Wextra -DVERSION=$(VERSION) -std=c++11 + +DESTDIR = /usr/local + +all: libkmer.so kmer_total_count kmer_counts_per_sequence kmer_utils.o \ + kmer_locations kmer_continuous_count + +getline.o: getline/getline.c + $(CC) -c getline/getline.c -o getline.o $(CFLAGS) + +kmer_utils.o: kmer_utils.c getline.o + $(CC) -c kmer_utils.c getline.o -O $(CFLAGS) -fPIC -DFORCE_GETLINE=1 + +libkmer.so: kmer_utils.o getline.o + $(CC) getline.o kmer_utils.o -o libkmer.so $(CFLAGS) -shared -fPIC + +kmer_total_count: kmer_utils.o kmer_total_count.c kmer_utils.h + $(CC) getline.o kmer_utils.o kmer_total_count.c -o kmer_total_count $(CLIBS) $(CFLAGS) + +kmer_counts_per_sequence: kmer_utils.o kmer_counts_per_sequence.c kmer_utils.h + $(CC) getline.o kmer_utils.o kmer_counts_per_sequence.c -o kmer_counts_per_sequence $(CLIBS) $(CFLAGS) -DFORCE_GETLINE=1 + +kmer_continuous_count: kmer_utils.o kmer_continuous_count.c kmer_utils.h + $(CC) getline.o kmer_utils.o kmer_continuous_count.c -o kmer_continuous_count $(CLIBS) $(CFLAGS) + +kmer_locations: kmer_utils.o kmer_locations.c kmer_utils.h + $(CC) getline.o kmer_utils.o kmer_locations.c -o kmer_locations $(CLIBS) $(CFLAGS) -DFORCE_GETLINE=1 +clean: + rm -vf kmer_total_count kmer_counts_per_sequence kmer_continuous_count \ + kmer_utils.o libkmer.so kmer_locations getline.o + +debug: CFLAGS = -ggdb -Wall -Wextra -DVERSION=$(VERSION)\"-debug\" -std=c++11 +debug: all + +install: all + install kmer_counts_per_sequence $(DESTDIR)/bin + install kmer_total_count $(DESTDIR)/bin + install kmer_continuous_count $(DESTDIR)/bin + install kmer_locations $(DESTDIR)/bin + cp -vf libkmer.so $(DESTDIR)/lib/ + diff --git a/getline/getdelim.c b/getline/getdelim.c new file mode 100644 index 0000000..8498b75 --- /dev/null +++ b/getline/getdelim.c @@ -0,0 +1,119 @@ +/* getdelim.c --- Implementation of replacement getdelim function. + Copyright (C) 1994, 1996, 1997, 1998, 2001, 2003, 2005 Free + Software Foundation, Inc. + + 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, 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, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301, USA. */ + +/* Ported from glibc by Simon Josefsson. */ + +#ifdef HAVE_CONFIG_H +# include <config.h> +#endif + +#include <stdlib.h> +#include <errno.h> + +#include "getdelim.h" + +#if !HAVE_FLOCKFILE +# undef flockfile +# define flockfile(x) ((void) 0) +#endif +#if !HAVE_FUNLOCKFILE +# undef funlockfile +# define funlockfile(x) ((void) 0) +#endif + +/* Read up to (and including) a DELIMITER from FP into *LINEPTR (and + NUL-terminate it). *LINEPTR is a pointer returned from malloc (or + NULL), pointing to *N characters of space. It is realloc'ed as + necessary. Returns the number of characters read (not including + the null terminator), or -1 on error or EOF. */ + +ssize_t +getdelim (char **lineptr, size_t *n, int delimiter, FILE *fp) +{ + int result = 0; + ssize_t cur_len = 0; + ssize_t len; + + if (lineptr == NULL || n == NULL || fp == NULL) + { + errno = EINVAL; + return -1; + } + + flockfile (fp); + + if (*lineptr == NULL || *n == 0) + { + *n = 120; + *lineptr = (char *) malloc (*n); + if (*lineptr == NULL) + { + result = -1; + goto unlock_return; + } + } + + for (;;) + { + char *t; + int i; + + i = getc (fp); + if (i == EOF) + { + result = -1; + break; + } + + /* Make enough space for len+1 (for final NUL) bytes. */ + if (cur_len + 1 >= *n) + { + size_t needed = 2 * (cur_len + 1) + 1; /* Be generous. */ + char *new_lineptr; + + if (needed < cur_len) + { + result = -1; + goto unlock_return; + } + + new_lineptr = (char *) realloc (*lineptr, needed); + if (new_lineptr == NULL) + { + result = -1; + goto unlock_return; + } + + *lineptr = new_lineptr; + *n = needed; + } + + (*lineptr)[cur_len] = i; + cur_len++; + + if (i == delimiter) + break; + } + (*lineptr)[cur_len] = '\0'; + result = cur_len ? cur_len : result; + + unlock_return: + funlockfile (fp); + return result; +} diff --git a/getline/getdelim.h b/getline/getdelim.h new file mode 100644 index 0000000..8bc6130 --- /dev/null +++ b/getline/getdelim.h @@ -0,0 +1,28 @@ +/* getdelim.h --- Prototype for replacement getdelim function. + Copyright (C) 2005 Free Software Foundation, Inc. + + 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, 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, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301, USA. */ + +/* Written by Simon Josefsson. */ + +/* Get size_t, FILE, ssize_t. And getdelim, if available. */ +# include <stddef.h> +# include <stdio.h> +# include <sys/types.h> + +#if !HAVE_DECL_GETDELIM +ssize_t getdelim (char **lineptr, size_t *n, int delimiter, FILE *stream); +#endif /* !HAVE_GETDELIM */ diff --git a/getline/getline.c b/getline/getline.c new file mode 100644 index 0000000..889cfe0 --- /dev/null +++ b/getline/getline.c @@ -0,0 +1,152 @@ +/* getline.c --- Implementation of replacement getline function. + Copyright (C) 2005 Free Software Foundation, Inc. + + 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, 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, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301, USA. */ + +/* Written by Simon Josefsson. */ + +#ifdef HAVE_CONFIG_H +# include <config.h> +#endif + +#include "getdelim.h" +#include "getline.h" + +ssize_t +getline (char **lineptr, size_t *n, FILE *stream) +{ + return getdelim (lineptr, n, '\n', stream); +} + +/* getdelim.c --- Implementation of replacement getdelim function. + Copyright (C) 1994, 1996, 1997, 1998, 2001, 2003, 2005 Free + Software Foundation, Inc. + + 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, 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, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301, USA. */ + +/* Ported from glibc by Simon Josefsson. */ + +#ifdef HAVE_CONFIG_H +# include <config.h> +#endif + +#include <stdlib.h> +#include <errno.h> + +#include "getdelim.h" + +#if !HAVE_FLOCKFILE +# undef flockfile +# define flockfile(x) ((void) 0) +#endif +#if !HAVE_FUNLOCKFILE +# undef funlockfile +# define funlockfile(x) ((void) 0) +#endif + +/* Read up to (and including) a DELIMITER from FP into *LINEPTR (and + NUL-terminate it). *LINEPTR is a pointer returned from malloc (or + NULL), pointing to *N characters of space. It is realloc'ed as + necessary. Returns the number of characters read (not including + the null terminator), or -1 on error or EOF. */ + +ssize_t +getdelim (char **lineptr, size_t *n, int delimiter, FILE *fp) +{ + int result = 0; + ssize_t cur_len = 0; + ssize_t len; + + if (lineptr == NULL || n == NULL || fp == NULL) + { + errno = EINVAL; + return -1; + } + + flockfile (fp); + + if (*lineptr == NULL || *n == 0) + { + *n = 120; + *lineptr = (char *) malloc (*n); + if (*lineptr == NULL) + { + result = -1; + goto unlock_return; + } + } + + for (;;) + { + char *t; + int i; + + i = getc (fp); + if (i == EOF) + { + result = -1; + break; + } + + /* Make enough space for len+1 (for final NUL) bytes. */ + if (cur_len + 1 >= *n) + { + size_t needed = 2 * (cur_len + 1) + 1; /* Be generous. */ + char *new_lineptr; + + if (needed < cur_len) + { + result = -1; + goto unlock_return; + } + + new_lineptr = (char *) realloc (*lineptr, needed); + if (new_lineptr == NULL) + { + result = -1; + goto unlock_return; + } + + *lineptr = new_lineptr; + *n = needed; + } + + (*lineptr)[cur_len] = i; + cur_len++; + + if (i == delimiter) + break; + } + (*lineptr)[cur_len] = '\0'; + result = cur_len ? cur_len : result; + + unlock_return: + funlockfile (fp); + return result; +} diff --git a/getline/getline.h b/getline/getline.h new file mode 100644 index 0000000..17efc23 --- /dev/null +++ b/getline/getline.h @@ -0,0 +1,53 @@ +/* getline.h --- Prototype for replacement getline function. + Copyright (C) 2005 Free Software Foundation, Inc. + + 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, 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, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301, USA. */ + +/* Written by Simon Josefsson. */ + +/* Get size_t, FILE, ssize_t. And getline, if available. */ +# include <stddef.h> +# include <stdio.h> +# include <sys/types.h> + +ssize_t getline (char **lineptr, size_t *n, FILE *stream); + +/* getdelim.h --- Prototype for replacement getdelim function. + Copyright (C) 2005 Free Software Foundation, Inc. + + 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, 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, write to the Free Software + Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA + 02110-1301, USA. */ + +/* Written by Simon Josefsson. */ + +/* Get size_t, FILE, ssize_t. And getdelim, if available. */ +# include <stddef.h> +# include <stdio.h> +# include <sys/types.h> + +ssize_t getdelim (char **lineptr, size_t *n, int delimiter, FILE *stream); diff --git a/kmer_counts_per_sequence.c b/kmer_counts_per_sequence.c index e9ca812..95f57fa 100644 --- a/kmer_counts_per_sequence.c +++ b/kmer_counts_per_sequence.c @@ -8,6 +8,10 @@ #include "kmer_utils.h" +#ifdef FORCE_GETLINE + #include "getline/getline.h" +#endif + void help() { printf("usage: kmer_counts_per_sequence input_file kmer [kmer-file] ...\n\n" "count mers in each sequence of size k from a fasta file\n" diff --git a/kmer_locations.c b/kmer_locations.c index e118b9f..10c5339 100644 --- a/kmer_locations.c +++ b/kmer_locations.c @@ -8,6 +8,10 @@ #include "kmer_utils.h" +#ifdef FORCE_GETLINE + #include "getline/getline.h" +#endif + void print_mer(unsigned long long mer, const long long pos, const bool labels, const bool reverse, unsigned int kmer, char *label) { if(labels) { char *kmer_str; diff --git a/kmer_total_count.c b/kmer_total_count.c index c3ae070..6f1c8ee 100644 --- a/kmer_total_count.c +++ b/kmer_total_count.c @@ -1,8 +1,8 @@ // Copyright 2013 Calvin Morrison #include <errno.h> #include <stdbool.h> -#include <stdio.h> -#include <stdlib.h> +#include <cstdio> +#include <cstdlib> #include <string.h> #include <getopt.h> diff --git a/kmer_utils.c b/kmer_utils.c index a154cb2..be547dc 100644 --- a/kmer_utils.c +++ b/kmer_utils.c @@ -9,6 +9,10 @@ using namespace std; +#ifdef FORCE_GETLINE + #include "getline/getline.h" +#endif + typedef struct { size_t operator() (const size_t &k) const { return k; |