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FFindex was designed and implemented by Andreas Hauser <andy@splashground.de>.
Please add your name here if you distribute modified versions.
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README
View file @ 6599a15d
* Copyright
FFindex was written by Andreas Hauser <andy@splpashground.de>.
FFindex was written by Andreas Hauser <Andreas.Hauser@LMU.de>.
Please add your name here if you distribute modified versions.
FFindex is provided under the Create Commons license "Attribution-ShareAlike 3.0",
FFindex is provided under the Create Commons license "Attribution-ShareAlike 4.0",
which basically captures the spirit of the Gnu Public License (GPL).
See:
http://creativecommons.org/licenses/by-sa/3.0/
http://creativecommons.org/licenses/by-sa/4.0/
* Thanks
......
RELEASE_NOTES
View file @ 6599a15d
For updated version, please see public git log.
0.9.9.6
- Fix OS X builds and integrate Makefile.osx
......
debian/changelog
View file @ 6599a15d
ffindex (0.9.9.9-1) unstable; urgency=medium
* New upstream version
-- Andreas Tille <tille@debian.org> Mon, 28 Jan 2019 19:03:23 +0100
ffindex (0.9.9.8-1) unstable; urgency=medium
* Revert again to original code which now added the interface for
......
debian/patches/Makefile.patch
View file @ 6599a15d
......@@ -40,7 +40,7 @@ Last-Update: 2017-06-29
FFINDEX_HEADERS=ffindex.h ffindex_posix_search.h ffutil.h
FFINDEX_OBJECTS=$(FFINDEX_HEADERS:.h=.o)
@@ -34,30 +39,30 @@ libffindex.a: $(FFINDEX_OBJECTS)
@@ -34,30 +39,29 @@ libffindex.a: $(FFINDEX_OBJECTS)
ar rcs libffindex.a $^
ifeq ($(OS), Darwin)
......@@ -50,9 +50,11 @@ Last-Update: 2017-06-29
+ $(CC) -shared -o libffindex.so.$(SOVERSION) $^
else
ifdef FFINDEX_STATIC
STATIC=-static
endif
- ifdef FFINDEX_STATIC
-STATIC=-static
- endif
+# Hack in needed linker options into unneeded variable STATIC
+STATIC=-L. -lffindex
-libffindex.so.0.1: $(FFINDEX_OBJECTS)
- $(CC) -Wl,-z,defs -Wl,-soname,libffindex.so.0.1 -shared -o libffindex.so.0.1 $^
......@@ -79,39 +81,16 @@ Last-Update: 2017-06-29
ffindex_apply_mpi.o: ffindex_apply_mpi.c $(FFINDEX_HEADERS)
mpicc $(CFLAGS) -DHAVE_MPI -c ffindex_apply_mpi.c -o $@
@@ -69,24 +74,24 @@ ffindex_apply_mpi_spawn.o: ffindex_apply
mpicc $(CFLAGS) -c ffindex_apply_mpi_spawn.c -o $@
ffindex_from_fasta: ffindex_from_fasta.o $(FFINDEX_LIBS)
- $(CC) -o $@ ffindex_from_fasta.o $(LDFLAGS) $(STATIC)
+ $(CC) -o $@ ffindex_from_fasta.o $(LDFLAGS) -L. -lffindex
ffindex_from_tsv: ffindex_from_tsv.o $(FFINDEX_LIBS)
- $(CC) -o $@ ffindex_from_tsv.o $(LDFLAGS) $(STATIC)
+ $(CC) -o $@ ffindex_from_tsv.o $(LDFLAGS) -L. -lffindex
ffindex_get: ffindex_get.o $(FFINDEX_LIBS)
- $(CC) -o $@ ffindex_get.o $(LDFLAGS) $(STATIC)
+ $(CC) -o $@ ffindex_get.o $(LDFLAGS) -L. -lffindex
ffindex_build: ffindex_build.o $(FFINDEX_LIBS)
- $(CC) -o $@ ffindex_build.o $(LDFLAGS) $(STATIC)
+ $(CC) -o $@ ffindex_build.o $(LDFLAGS) -L. -lffindex
ffindex_modify: ffindex_modify.o $(FFINDEX_LIBS)
- $(CC) -o $@ ffindex_modify.o $(LDFLAGS) $(STATIC)
+ $(CC) -o $@ ffindex_modify.o $(LDFLAGS) -L. -lffindex
ffindex_unpack: ffindex_unpack.o $(FFINDEX_LIBS)
- $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
+ $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) -L. -lffindex
@@ -89,7 +93,7 @@ ffindex_unpack: ffindex_unpack.o $(FFIND
ffindex_order: ffindex_order.o $(FFINDEX_LIBS)
$(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
-test:
+check:
rm -f /tmp/test.data /tmp/test.ffindex
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_get /tmp/test.data /tmp/test.ffindex a b foo | tee /tmp/test.out
@@ -107,9 +112,10 @@ time:
@@ -110,9 +114,10 @@ time:
clean:
rm -f $(FFINDEX_PROGRAMS) $(FFINDEX_OBJECTS) $(FFINDEX_LIBS) \
......@@ -124,7 +103,7 @@ Last-Update: 2017-06-29
install:
mkdir -p $(INSTALL_DIR)/bin
@@ -122,9 +128,10 @@ install:
@@ -125,9 +130,10 @@ install:
install ffindex_from_tsv $(INSTALL_DIR)/bin/ffindex_from_tsv
install ffindex_apply $(INSTALL_DIR)/bin/ffindex_apply
install ffindex_unpack $(INSTALL_DIR)/bin/ffindex_unpack
......@@ -137,7 +116,7 @@ Last-Update: 2017-06-29
install ffindex.h $(INSTALL_DIR)/include/ffindex.h
install ffutil.h $(INSTALL_DIR)/include/ffutil.h
install ffindex_posix_search.h $(INSTALL_DIR)/include/ffindex_posix_search.h
@@ -134,7 +141,7 @@ endif
@@ -137,7 +143,7 @@ endif
deinstall:
rm -f $(INSTALL_DIR)/bin/ffindex_get $(INSTALL_DIR)/bin/ffindex_build $(INSTALL_DIR)/bin/ffindex_modify \
......
debian/patches/basename.patch
View file @ 6599a15d
......@@ -48,21 +48,10 @@ Forwarded: yes
-/* vim: ts=2 sw=2 et: */
+// vim: ts=2 sw=2 et:
--- a/src/ffindex_unpack.c
+++ b/src/ffindex_unpack.c
@@ -37,7 +37,7 @@ int main(int argn, char **argv)
fprintf(stderr, "USAGE: %s DATA_FILENAME INDEX_FILENAME OUT_DIR\n"
"\n\tPlease note that a huge number of files might be created!\n"
FFINDEX_COPYRIGHT,
- argv[0]);
+ basename(argv[0]));
return -1;
}
char *data_filename = argv[1];
--- a/src/ffindex.h
+++ b/src/ffindex.h
@@ -24,6 +24,8 @@
#define FFINDEX_VERSION 0.998
#define FFINDEX_VERSION 0.999
#define FFINDEX_COPYRIGHT "\nDesigned and implemented by Andreas Hauser <andy@splashground.de>.\n"
+// lkajan: the below makes a default allocation over 2G. malloc in ffindex.c:225 fails on a machine with 'only' 2G of RAM.
......@@ -79,19 +68,6 @@ Forwarded: yes
int ffindex_insert_memory(FILE *data_file, FILE *index_file, size_t *offset, char *from_start, size_t from_length, char *name);
int ffindex_insert_file(FILE *data_file, FILE *index_file, size_t *offset, const char *path, char *name);
--- a/src/ffindex_apply_mpi.c
+++ b/src/ffindex_apply_mpi.c
@@ -214,8 +214,8 @@ int main(int argn, char **argv)
"\t-d\tFFDATA output file, stdout of program will be captured\n"
"\t-i\tFFINDEX output file, entries get the same name as input entry\n"
FFINDEX_COPYRIGHT,
- argv[0],
- argv[0]);
+ basename(argv[0]),
+ basename(argv[0]));
errno = EINVAL;
goto EXCEPTION;
}
--- a/src/ffindex_get.c
+++ b/src/ffindex_get.c
@@ -29,8 +29,10 @@ void usage(char* program_name)
......
rpm/ffindex.spec
View file @ 6599a15d
Summary: FFindex is a very simple index/database for huge amounts of small files.
Name: ffindex
Version: 0.9.9.8
Version: 0.9.9.9
Release: 1
License: Create Commons license "Attribution-ShareAlike 3.0"
Group: Utilities/System
Source: https://github.com/ahcm/ffindex/archive/0.9.9.8.tar.gz
Source: https://github.com/ahcm/ffindex/archive/0.9.9.9.tar.gz
%description
FFindex is a very simple index/database for huge amounts of small files. The
files are stored concatenated in one big data file, seperated by '\0'. A second
......
src/Makefile
View file @ 6599a15d
......@@ -86,6 +86,9 @@ ffindex_modify: ffindex_modify.o $(FFINDEX_LIBS)
ffindex_unpack: ffindex_unpack.o $(FFINDEX_LIBS)
$(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
ffindex_order: ffindex_order.o $(FFINDEX_LIBS)
$(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
test:
rm -f /tmp/test.data /tmp/test.ffindex
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2
......
src/ffindex.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
......
src/ffindex.h
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*
* Ffindex is a very simple database for small files. The files are stored
* concatenated in one big data file, seperated by '\0'. A second file
......@@ -21,7 +21,7 @@
#include <stdio.h>
#define FFINDEX_VERSION 0.998
#define FFINDEX_VERSION 0.999
#define FFINDEX_COPYRIGHT "\nDesigned and implemented by Andreas Hauser <andy@splashground.de>.\n"
#define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 80000000
......
src/ffindex_apply_mpi.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*
* ffindex_apply
* apply a program to each FFindex entry
......@@ -214,8 +214,8 @@ int main(int argn, char **argv)
"\t-d\tFFDATA output file, stdout of program will be captured\n"
"\t-i\tFFINDEX output file, entries get the same name as input entry\n"
FFINDEX_COPYRIGHT,
argv[0],
argv[0]);
basename(argv[0]),
basename(argv[0]));
errno = EINVAL;
goto EXCEPTION;
}
......
src/ffindex_apply_mpi_spawn.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*
* ffindex_apply
* apply a program to each FFindex entry
......
src/ffindex_build.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
......
src/ffindex_from_fasta.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
......@@ -60,7 +60,7 @@ int main(int argn, char **argv)
version = 1;
break;
default:
usage(argv[0]);
usage(basename(argv[0]));
return EXIT_FAILURE;
}
}
......@@ -74,7 +74,7 @@ int main(int argn, char **argv)
if(argn - optind < 3)
{
usage(argv[0]);
usage(basename(argv[0]));
return EXIT_FAILURE;
}
......
src/ffindex_from_tsv.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
......
src/ffindex_get.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
......@@ -70,6 +70,7 @@ int main(int argn, char **argv)
ffindex_db->ffdata_filename = data_filename;
ffindex_db->ffindex_filename = index_filename;
ffindex_db->mode[0] = 'r';
ffindex_db->num_max_entries = ffcount_lines(index_filename);
ffindex_db = ffindex_index_db_open(ffindex_db);
if(!ffindex_db)
......
src/ffindex_modify.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
......@@ -71,7 +71,7 @@ int main(int argn, char **argv)
break;
default:
fprintf(stderr, "Option %c not recognized\n", opt);
usage(argv[0]);
usage(basename(argv[0]));
return EXIT_FAILURE;
}
}
......
src/ffindex_optimize.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
......
src/ffindex_unpack.c
View file @ 6599a15d
......@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
* 3.0", which basically captures the spirit of the Gnu Public License (GPL).
* 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
* http://creativecommons.org/licenses/by-sa/3.0/
* http://creativecommons.org/licenses/by-sa/4.0/
*
* ffindex_apply
* apply a program to each FFindex entry
......@@ -37,7 +37,7 @@ int main(int argn, char **argv)
fprintf(stderr, "USAGE: %s DATA_FILENAME INDEX_FILENAME OUT_DIR\n"
"\n\tPlease note that a huge number of files might be created!\n"
FFINDEX_COPYRIGHT,
argv[0]);
basename(argv[0]));
return -1;
}
char *data_filename = argv[1];
......