Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/.dockerignore
+++ b/.dockerignore
-.git/
-.idea/
-bin/
-build/
-test/
-cmake-build-debug/
-cmake-build-release/
--- a/.gitignore
+++ b/.gitignore
-# Object files
-*.o
-*.ko
-*.obj
-*.elf
-
-# Libraries
-*.lib
-*.a
-
-# Shared objects (inc. Windows DLLs)
-*.dll
-*.so
-*.so.*
-*.dylib
-
-# Executables
-*.exe
-*.out
-*.app
-*.i*86
-*.x86_64
-*.hex
-
-# Build directory
-/build
--- a/.hgignore
+++ b/.hgignore
+.*\.o
+test_big
+bin
+lib
+include
--- a/.travis.yml
+++ b/.travis.yml
-# Ubuntu 14.04 Trusty support
-sudo: required
-dist: trusty
-
-addons:
-  apt:
-    packages:
-    - cmake
-
-before_install:
- git submodule update --init --recursive
-
-script:
- mkdir build
- cd build
- cmake .. && make
-# - CTEST_OUTPUT_ON_FAILURE=TRUE make test
-
-
-matrix:
-  include:
-    - compiler: gcc
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.9
-            - mpi-default-dev
-      env: CXX=g++-4.9
-    - compiler: gcc
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-5
-            - mpi-default-dev
-      env: CXX=g++-5
-    - compiler: gcc
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-6
-            - mpi-default-dev
-      env: CXX=g++-6
-    - compiler: clang
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-            - llvm-toolchain-precise-3.6
-          packages:
-            - clang-3.6
-            - mpi-default-dev
-      env: CXX=clang++-3.6
-    - compiler: clang
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-            - llvm-toolchain-precise-3.7
-          packages:
-            - clang-3.7
-            - mpi-default-dev
-      env: CXX=clang++-3.7
-    - compiler: clang
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-            - llvm-toolchain-precise-3.8
-          packages:
-            - clang-3.8
-            - mpi-default-dev
-      env: CXX=clang++-3.8
-
-
-
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-cmake_minimum_required(VERSION 2.8.12 FATAL_ERROR)
-SET(HAVE_MPI 1 CACHE BOOL "Have MPI")
-
-project(ffindex C)
-include_directories(src)
-include_directories(src/ext)
-add_subdirectory(src)
-
--- a/Dockerfile
+++ b/Dockerfile
-FROM alpine:latest as ffindex-builder
-
-RUN apk add --no-cache gcc cmake musl-dev ninja
-
-WORKDIR /opt/ffindex
-ADD . .
-
-WORKDIR build
-RUN cmake -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..
-RUN ninja && ninja install
-
-FROM alpine:latest
-MAINTAINER Milot Mirdita <milot@mirdita.de>
-RUN apk add --no-cache gawk bash grep libstdc++
-
-COPY --from=ffindex-builder /opt/ffindex/build/bin /usr/local/bin/
--- a/LICENSE
+++ b/LICENSE
 AUTHOR

-FFindex was designed and implemented by Andreas Hauser <hauser@genzentrum.lmu.de>.
+FFindex was designed and implemented by Andreas Hauser <andy@splashground.de>.
 Please add your name here if you distribute modified versions.

 This file must be distributed with any source or binary distribution including
-parts of this work.
+parts of this work, excempt ffutil.h and ffutil.c which are also available
+under MIT license.

 SHORT SUMMARY OF THE LICENSE

-Ffindex is provided under the Create Commons license "Attribution-ShareAlike
+FFindex is provided under the Create Commons license "Attribution-ShareAlike
 3.0", which basically captures the spirit of the Gnu Public License (GPL).

 See:

--- a/Makefile
+++ b/Makefile
+all:
+	$(MAKE) -C src $@
+
+%:
+	$(MAKE) -C src $@
+
+release:
+	git archive HEAD --prefix "ffindex-`cat VERSION`/" -o "ffindex-`cat VERSION`.tar.gz"
+
+relnotes:
+	git log --pretty=format:" - %s%n%b" 
--- a/README.md
+++ b/README.md
-# FFindex - A database wrapped around mmap
-
-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
-file contains a plain text index, giving name, offset and length of of the
-small files. The lookup is currently done with a binary search on an array made
-from the index file. The attatched binaries (see Usage below) and their source
-code shall give an impression of how to use the functions supported by the library in C/C++ code.
- 
-## Copyright
-
-FFindex was written by Andreas Hauser <hauser@genzentrum.lmu.de>.
+* Copyright

+FFindex was written by Andreas Hauser <andy@splpashground.de>.
 Please add your name here if you distribute modified versions.
-* Martin Steinegger <martin.steinegger@mpibpc.mpg.de>
-* Markus Meier <markus.meier@mpibpc.mpg.de>

 FFindex is provided under the Create Commons license "Attribution-ShareAlike 3.0",
 which basically captures the spirit of the Gnu Public License (GPL).
@@ -21,86 +9,85 @@ which basically captures the spirit of the Gnu Public License (GPL).
 See:
 http://creativecommons.org/licenses/by-sa/3.0/

-[ ![Codeship Status for soedinglab/ffindex](https://codeship.com/projects/6c26cd00-2247-0133-1269-52bb0fef976f/status?branch=master)](https://codeship.com/projects/96084)
-[ ![Build Status](https://travis-ci.org/soedinglab/hh-suite.svg?branch=master)](https://travis-ci.org/soedinglab/ffindex_soedinglab)
-
-## Thanks
+* Thanks

 Thanks to Laszlo Kajan for creating and maintaining Debian packages
 and many suggestions to improve the build and user experience.


+* Overview
+
+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
+file contains a plain text index, giving name, offset and length of of the
+small files. The lookup is currently done with a binary search on an array made
+from the index file.
+
+
+* Installation
 
-## Installation
+$ cd src
+$ make
+$ make test

-### Compilation
-With the sourcecode ready, simply run cmake with the default settings and libraries should be auto-detected:
+If you have MPI and want to compile ffindex_apply_mpi:
+$ make HAVE_MPI=1

-	mkdir build
-	cd build
-	cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=${INSTALL_BASE_DIR} ..
-	make
-	make install
+On OS X use for the first make line:
+$ make -f Makefile.osx

+# Please use a sensible value for INSTALL_DIR, e.g. /usr/local or /opt/ffindex
+# or $HOME/ffindex instead of "..".
+$ make install INSTALL_DIR=.. 

-**Please use a sensible value for ${INSTALL_BASE_DIR}, e.g. /usr/local or /opt/ffindex or $HOME/ffindex**
+and with MPI:

+$ make install INSTALL_DIR=.. HAVE_MPI=1

-### Setting environment variables
+
+* Usage

 Please note that before querying or unlinking entries a ffindex must be
 sorted, although you can add to it without. So either specify -s with
 ffindex_build or sorted later with ffindex_modify -s.
+Also the length of the entry names is restricted. See the usage output of
+the ffindex_build program.

 Setup environment:
-
-	export PATH="${INSTALL_BASE_DIR}/bin:${PATH}"
-	export LD_LIBRARY_PATH="${INSTALL_BASE_DIR}/lib:${LD_LIBRARY_PATH}"
+$ export PATH="$INSTALL_DIR/bin:$PATH"
+$ export LD_LIBRARY_PATH="$INSTALL_DIR/lib:$LD_LIBRARY_PATH"
 On OS X set DYLD_LIBRARY_PATH instead of LD_LIBRARY_PATH.

-## Usage
-
 Build index from files in test/data and test/data2.
-
-	ffindex_build -s /tmp/test.data /tmp/test.ffindex test/data test/data2
+$ ffindex_build -s /tmp/test.data /tmp/test.ffindex test/data test/data2

 Retrieve three entries:
-
-	ffindex_get  /tmp/test.data /tmp/test.ffindex a b foo
+$ ffindex_get  /tmp/test.data /tmp/test.ffindex a b foo

 Unlink (Remove reference from index) an entry:
-
-	ffindex_modify -u /tmp/test.ffindex b
+$ ffindex_modify -u /tmp/test.ffindex b

 Retrieve three entries, "b" should now be missing:
-
-	ffindex_get /tmp/test.data /tmp/test.ffindex a b foo
+$ ffindex_get /tmp/test.data /tmp/test.ffindex a b foo

 Convert a Fasta file to ffindex, entry names are incerental IDs starting from 1:
-
-	ffindex_from_fasta -s fasta.ffdata fasta.ffindex NC_007779.ffn
+$ ffindex_from_fasta -s fasta.ffdata fasta.ffindex NC_007779.ffn

 Get first entry by name:
-
-	ffindex_get fasta.ffdata fasta.ffindex 1
+$ ffindex_get fasta.ffdata fasta.ffindex 1

 Get first and third entry by entry index, this a little faster:
-
-	ffindex_get fasta.ffdata fasta.ffindex -n 1 3
+$ ffindex_get fasta.ffdata fasta.ffindex -n 1 3

 Count the characters including header in each entry:
-
-	ffindex_apply fasta.ffdata fasta.ffindex wc -c
+$ ffindex_apply fasta.ffdata fasta.ffindex wc -c

 Count the number of characters in each sequence, without the header:
-
-	ffindex_apply fasta.ffdata fasta.ffindex perl -ne '$x += length unless(/^>/); END{print "$x\n"}'
+$ ffindex_apply fasta.ffdata fasta.ffindex perl -ne '$x += length unless(/^>/); END{print "$x\n"}'

 Parallel version for counting the characters including header in each entry:
-
-	mpirun -np 4 ffindex_apply_mpi fasta.ffdata fasta.ffindex -- wc -c
+$ mpirun -np 4 ffindex_apply_mpi fasta.ffdata fasta.ffindex -- wc -c

 Parallel version for counting the characters including header in each entry and
 saving the output to a new ffindex:
-
-	mpirun -np 4 ffindex_apply_mpi fasta.ffdata fasta.ffindex -i out-wc.ffindex -o out-wc.ffdata -- wc -c
+$ mpirun -np 4 ffindex_apply_mpi fasta.ffdata fasta.ffindex -i out-wc.ffindex -d out-wc.ffdata -- wc -c
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
+0.9.9.6
+ - Fix OS X builds and integrate Makefile.osx
+
+ - Drop OpenMP from compiler flags
+
+ - Add ffindex_posix_search.o to make clean
+
+ - Avoid non-standard nested function, even so it's the cleanest solution,
+   since the posix twalk interface is broken. Factor out functions using posix
+   tree. Use TLS variables to stay threadsafe.
+
+ - Fix ffnchomp check
+
+0.9.9.5
+ - Make use of our parse_long for higher startup performance.
+
+ - Add RELEASE_NOTES
+
+ - Roll our own parse_ulong instead strtol for speed reasons.
+
+ - Fix usage formatting
+
+ - Make more clear that tree is already sorted ffindex_modify.c
+
+ - Remove unused code in ffindex_modify.c
+
+0.9.9.4 and before
+
+ - ffindex_apply is now ffindex_apply_mpi without MPI
+
+ - Add src/ffindex_apply_mpi_spawn.c, using spawn istead of fork & exec
+
+ - Fix example
+
+ - Add collect_data
+
+ - Add Markus Meier
+
+ - perl5/FFindex.pm: Add copyright. Fix entry reading. Add get_entry* methods.
+
+ - Add perl5/test.pl
+
+ - Add perl5
+
+ - Add each_data
+
+ - Return Qnil if not found
+
+ - Add method_ffindex_get_data_by_name
+
+ - Add first ruby wrapper.
+
+ - Add ffindex_db
+
+ - Add nginx server module
+
+ - Fix memory leak on error
+
+ - ffindex_get: Add -f FILE argument to let the keys to retrieve be specified by a file.
+
+ - Add ffindex_from_tsv to Makefile
+
+ - Add ffindex_from_tsv
+
+ - Update RPM spec
+
+ - bump version
+
+ - Update copyrigths and version.
+
+ - Set higher limits. Update version.
+
+ - Handle the case where filenames are actually longer than FFINDEX_MAX_ENTRY_NAME_LENTH. This was also security vulnerability.
+
+ - fix fprintf
+
+ - Add log_file option to ffindex_apply_mpi and rework error handling.
+
+ - fix getopt
+
+ - merge
+
+ - Add ffindex_optimize
+
+ - bumb version
+
+ - Add -q for quiet
+
+ - merge
+
+ - Better usage info.
+
+ - Make sort work independant from unlink.
+
+ - Add ffindex_insert_ffindex().
+
+ - Make use of ffindex_index_open in ffindex_from_fasta
+
+ - Add ffindex_index_open() and use it in ffindex_build.
+
+ - Add -D_GNU_SOURCE=1, probably better here than in source.
+
+ - Bump version
+
+ - Export FFINDEX_ENTRY_NAME and unlink() temporary ffindexes in ffindex_apply_mpi.
+
+ - Print entry and return status of ffindex_apply_mpi to stderr. This allows for further processing based on return status.
+
+ - Add MPI to README
+
+ - Don't assume string data, make binary data work too.
+
+ - Add get_entry_by_name as alias for bsearch
+
+ - Fix build for some compilers
+
+ - Ma
+
+ - Another fix for noncapture and cleanup
+
+ - Fix no capture mode
+
+ - First beta of apply_mpi output catching to another ffindex
+
+ - wip
+
+ - wip
+
+ - apply_mpi now works with capturing output to another ffindex, but I/O can block.
+
+ - Better error message
+
+ - More clever root Makefile contributed by Laszlo.
+
+ - Add thanks
+
+ - Reduce FFINDEX_MAX_ENTRY_NAME_LENTH from 56 to 32 so that by default the malloced space for the index is <2GB. Suggested by Laszlo.
+
+ - Add message to indicated number of failed bytes.
+
+ - Bump version to 0.980
+
+ - Add ffindex_unpack to install and spec and bump version to 0.9.8
+
+ - More improvements to usage info for ffindex_build.
+
+ - Add better usage info to ffindex_build, proposed by Johannes.
+
+ - remove modifies -t from usage
+
+ - merge
+
+ - merge
+
+ - wip ffindex_apply_mpi.c
+
+ - Add ffindex_unpack to unpack all entries/files from an ffindex
+
+ - Bump version to 0.97
+
+ - Check index out of bounds for ffindex_get_entry_by_index
+
+ - Add some more usage examples to README
+
+ - Add option -n to ffindex_get to use entry index instead of entry name
+
+ - Add ifndef wrapper as suggested by Markus.
+
+ - Add return check for 1 byte fwrite.
+
+ - Don't access index before NULL check. Reporter: Laszlo Karjan.
+
+ - Bump version
+
+ - Diy OSX build
+
+ - Bump version to 0.9.6
+
+ - Fix bug data vs. filedata.
+
+ - Use optimized interface
+
+ - Fix comment
+
+ - Conditionalize MPI
+
+ - Bump version to 0.9.5.
+
+ - Refactor to handle entry lookup outside of ffindex_apply.
+
+ - Handling of left over.
+
+ - Add first implementation of ffindex_apply_mpi.c.
+
+ - Handle EPIPE.
+
+ - Add a first version of ffindex_apply, that executes a program for each entry in the ffindex.
+
+ - Reflect ffindex_fopen rename.
+
+ - Rename ffindex_fopen to ffindex_fopen_by_name. Add ffindex_fopen_by_entry and ffindex_get_data_by_entry.
+
+ - Add hgignore
+
+ - Clean also .o
+
+ - Add it also to osx
+
+ - Add ffindex_from_fasta to clean
+
+ - Install ffindex_from_fasta
+
+ - Improve error handling, especially with empty Index file.
+
+ - Add ffindex_get_data_by_index. And rename other ffindex_get functions to be more uniform.
+
+ - Use ffindex_get() instead of ffindex_fopen() in ffindex_get program.
+
+ - Add ffindex_get to get entry as string.
+
+ - Raise FFINDEX_MAX_INDEX_ENTRIES_DEFAULT from 6 million to 40 million
+
+ - Make sure ">" is after newline. Better code.
+
+ - Add -O2.
+
+ - Complete implementation of ffindex_from_fasta.
+
+ - Bump version to 0.94
+
+ - Sart implementation of ffindex_from_fasta
+
+ - Add ffindex_insert_memory().
+
+ - Improve README
+
+ - Bump version to 0.9.3
+
+ - merge
+
+ - Better make chdir
+
+ - Make usage of tree default in ffindex_modify.
+
+ - Make OSX compile again.
+
+ - basename() is in libgen.h on BSD.
+
+ - Clean ffutil.o too.
+
+ - Add deinstall target
+
+ - Fix spec libdir
+
+ - Fix libdir creation
+
+ - bump version
+
+ - Fix spec
+
+ - Respect lib64
+
+ - nicer
+
+ - Add a SPEC file for building an RPM package.
+
+ - Rework build a little. Build a static library libffindex.a too.
+
+ - Add top-level Makefile.
+
+ - Fix remaining printf.
+
+ - Fix size_t printfs. Use length modifier z.
+
+ - Bump version.
+
+ - Move textfiles to top.
+
+ - Add inclusion clause to LICENSE.
+
+ - Add advertisement.
+
+ - Fix fclose with ffindex_add_filestream.
+
+ - ffindex_build now can incorporate (merge) other ffindexes.
+
+ - Add -t to ffindex_modify, which tells ffindex to speedup unlinking using a tree.
+
+ - unlink: walk to lists implmentation
+
+ - Fix message
+
+ - Fix unlink.
+
+ - Fix OS X build
+
+ - Fix test
+
+ - Remove more strnlen. Introduce ffnchomp in ffutil that was renamed from fferror.
+
+ - Use strlen instead of strnlen. Sae case and BSD/OS X do not always have strnlen.
+
+ - fix includes
+
+ - little things
+
+ - better documentation
+
+ - Add possibility to add single files not only directories. TODO: Decide what should be the name in the index, that is should the whole path be part of the entry name.
+
+ - Make INSTALL_DIR usable.
+
+ - Add
+
+ - Add ffindex_modify that oprates on an existing index. E.g. for unlinking.
+
+ - Guard against overwriting existing index or data file
+
+ - Add ffindex_unlink
+
+ - better tests
+
+ - Better error handling
+
+ - comment
+
+ - Better error handling
+
+ - nicer error handling
+
+ - nicer error handling
+
+ - spell
+
+ - Better error handling and messages, especially if malloc failes.
+
+ - ffindex_index_parse now takes a second argument specifying the maximum number of entries. A default is used if 0 is specified.
+
+ - Add -v for version. Add -f for list_files.
+
+ - Small code improvement.
+
+ - Add fmemopen for Mac OS X.
+
+ - fix warnings
+
+ - Add install target.
+
+ - - Add license. - Add append and sort.
+
+ - Faster parsing. ffindex_mmap interface changed.
+
+ - Convert index to struct. Implement bsearch.
+
+ - Rest of data type conversion. Ffindex_build now takes offset return value, which is needed e.g. for multiple directory indexing.
+
+ - Change *data to from type void* to char* to avoid problems with pointer arithmetics.
+
+ - Add test for multiple directory indexing
+
+ - Add second test dir.
+
+ - Make Makefile more robust.
+
+ - Add more functions to header.
+
+ - ffindex_get now support multiple entry retrieves.
+
+ - Remoove debug extra newlines from ffindex_get output.
+
+ - Remove debug print.
+
+ - Add clean.
+
+ - Add a program to retrieve data from index.
+
+ - Fix parameter mixup. Add length to index.
+
+ - Add test
+
+ - ffindex_fopen
+
+ - wip
+
+ - primitive ffindex_get_offset
+
+ - use read
+
+ - init
--- a/VERSION
+++ b/VERSION
-0.9.9
+0.9.9.7
--- a/debian/changelog
+++ b/debian/changelog
+ffindex (0.9.9.7+sog+git20160415.14274c9-1) unstable; urgency=medium
+
+  * The previous location on Github was an improperly chosen fork
+    (see https://github.com/soedinglab/ffindex_soedinglab/issues/4)
+    Here the version is now named "0.9.9.7+sog" (Saved On Github)
+    to make it alphabethically later than the previous one.
+    Closes: #907624
+  * debhelper 11
+  * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille@debian.org>  Fri, 21 Dec 2018 08:39:13 +0100
+
 ffindex (0.9.9.7+soedinglab+git20180802.74550c8-1) unstable; urgency=medium

  * Fix watch file (version should actually be +git20171201.74550c8 but

--- a/debian/compat
+++ b/debian/compat
-10
+11
--- a/debian/control
+++ b/debian/control
@@ -4,13 +4,12 @@ Uploaders: Laszlo Kajan <lkajan@debian.org>,
           Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
               help2man,
               libopenmpi-dev,
               openmpi-bin,
-               chrpath,
-               cmake
-Standards-Version: 4.2.0
+               chrpath
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/ffindex
 Vcs-Git: https://salsa.debian.org/med-team/ffindex.git
 Homepage: http://www.splashground.de/~andy/programs/FFindex/

--- a/debian/docs
+++ b/debian/docs
-README.md
+README*
--- a/debian/libffindex0-dev.install
+++ b/debian/libffindex0-dev.install
 usr/include/*
 usr/lib/libffindex.a
 usr/lib/libffindex.so
-# not found
-#src/ffindex_posix_search.h usr/include
+src/ffindex_posix_search.h usr/include
--- a/debian/patches/BuildSharedLibraryWithSameSuffix.patch
+++ b/debian/patches/BuildSharedLibraryWithSameSuffix.patch
-Author: Steffen Moeller
-Last-Update: 2018-08-02 19:14:12 +0200
-Description: Fix building of shared lib
-
-Index: ffindex/src/CMakeLists.txt
-===================================================================
--- ffindex.orig/src/CMakeLists.txt
-+++ ffindex/src/CMakeLists.txt
-@@ -1,17 +1,32 @@
-+cmake_minimum_required(VERSION 3.11)
- set(CMAKE_C_FLAGS "-std=c99 ${CMAKE_C_FLAGS}")
- 
- # sets HAVE_FMEMOPEN
- add_subdirectory(ext)
- 
-add_library (ffindex ffindex.c ffutil.c)
-+# Adapted from https://stackoverflow.com/questions/2152077/is-it-possible-to-get-cmake-to-build-both-a-static-and-shared-version-of-the-sam
- 
-target_include_directories (ffindex PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
-+# this is the "object library" target: compiles the sources only once
-+add_library(objlib OBJECT ffindex.c ffutil.c)
-+target_include_directories (objlib PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
-+
-+# shared libraries need PIC
-+set_property(TARGET objlib PROPERTY POSITION_INDEPENDENT_CODE 1)
-+
-+# shared and static libraries built from the same object files
-+add_library(ffindex-static STATIC $<TARGET_OBJECTS:objlib>)
-+add_library(ffindex-shared SHARED $<TARGET_OBJECTS:objlib>)
-+
-+set_target_properties(ffindex-static PROPERTIES OUTPUT_NAME ffindex)
-+
-+set_target_properties(ffindex-shared PROPERTIES VERSION 0.9.9.7
-+                                                SOVERSION 0
-+                                                OUTPUT_NAME ffindex)
- 
-add_library (ffindex_shared SHARED ffindex.c ffutil.c)
- 
- if(NOT HAVE_FMEMOPEN)
-        target_link_libraries(ffindex ext)
-        target_link_libraries(ffindex_shared ext)
-+#        target_link_libraries(ffindex ext)
-+        target_link_libraries(ffindex-shared ext)
- endif()
- 
- 
-@@ -19,7 +34,7 @@ endif()
- add_executable(ffindex_apply
-         ffindex_apply_mpi.c
- )
-target_link_libraries (ffindex_apply ffindex)
-+target_link_libraries (ffindex_apply ffindex-shared)
- set_property(TARGET ffindex_apply PROPERTY COMPILE_FLAGS "-UHAVE_MPI")
- 
- find_package(MPI)
-@@ -27,7 +42,7 @@ if(MPI_C_FOUND AND HAVE_MPI)
-     add_executable(ffindex_apply_mpi
-       ffindex_apply_mpi.c
-     )
-    target_link_libraries (ffindex_apply_mpi ffindex)
-+    target_link_libraries (ffindex_apply_mpi ffindex-shared)
-     add_subdirectory(mpq)
- 
-     set_property(TARGET ffindex_apply_mpi PROPERTY COMPILE_FLAGS "-DHAVE_MPI=1 ${MPI_C_COMPILE_FLAGS}")
-@@ -45,48 +60,48 @@ endif()
- add_executable(ffindex_reduce
-         ffindex_reduce.c
- )
-target_link_libraries (ffindex_reduce ffindex)
-+target_link_libraries (ffindex_reduce ffindex-shared)
- 
- add_executable(ffindex_build
-   ffindex_build.c
- )
-target_link_libraries (ffindex_build ffindex)
-+target_link_libraries (ffindex_build ffindex-shared)
- 
- 
- add_executable(ffindex_from_fasta
-   ffindex_from_fasta.c
- )
-target_link_libraries (ffindex_from_fasta ffindex)
-+target_link_libraries (ffindex_from_fasta ffindex-shared)
- 
- 
- add_executable(ffindex_get
-   ffindex_get.c
- )
-target_link_libraries (ffindex_get ffindex)
-+target_link_libraries (ffindex_get ffindex-shared)
- 
- 
- add_executable(ffindex_modify
-   ffindex_modify.c
- )
-target_link_libraries (ffindex_modify ffindex)
-+target_link_libraries (ffindex_modify ffindex-shared)
- 
- 
- add_executable(ffindex_unpack
-   ffindex_unpack.c
- )
-target_link_libraries (ffindex_unpack ffindex)
-+target_link_libraries (ffindex_unpack ffindex-shared)
- 
- 
- add_executable(ffindex_order
-   ffindex_order.c
- )
-target_link_libraries (ffindex_order ffindex)
-+target_link_libraries (ffindex_order ffindex-shared)
- 
- 
- add_executable(ffindex_from_fasta_with_split
-     ffindex_from_fasta_with_split.c
- )
-target_link_libraries (ffindex_from_fasta_with_split ffindex)
-+target_link_libraries (ffindex_from_fasta_with_split ffindex-shared)
- 
- 
- install(PROGRAMS 
-@@ -95,15 +110,15 @@ install(PROGRAMS
-         DESTINATION include
- )
- 
-install(TARGETS ffindex
-  LIBRARY DESTINATION lib64 COMPONENT libraries
-        ARCHIVE DESTINATION lib64 COMPONENT libraries
-+install(TARGETS ffindex-static
-+  LIBRARY DESTINATION lib COMPONENT libraries
-+        ARCHIVE DESTINATION lib COMPONENT libraries
- )
- 
- 
-install(TARGETS ffindex_shared
-  LIBRARY DESTINATION lib64 COMPONENT libraries
-        ARCHIVE DESTINATION lib64 COMPONENT libraries
-+install(TARGETS ffindex-shared
-+  LIBRARY DESTINATION lib COMPONENT libraries
-+        ARCHIVE DESTINATION lib COMPONENT libraries
- )
- 
- 
--- a/debian/patches/Makefile.patch
+++ b/debian/patches/Makefile.patch
@@ -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 @@
+@@ -34,30 +39,30 @@ libffindex.a: $(FFINDEX_OBJECTS)
 	ar rcs libffindex.a $^
 
 ifeq ($(OS), Darwin)
@@ -79,7 +79,7 @@ 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 @@
+@@ -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 $(FFINDEX_LIBS)
@@ -111,7 +111,7 @@ Last-Update: 2017-06-29
 	rm -f /tmp/test.data /tmp/test.ffindex
 	LD_LIBRARY_PATH=".:$(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 @@
+@@ -107,9 +112,10 @@ time:
 
 clean:
 	rm -f $(FFINDEX_PROGRAMS) $(FFINDEX_OBJECTS) $(FFINDEX_LIBS) \
@@ -124,7 +124,7 @@ Last-Update: 2017-06-29
 
 install:
 	mkdir -p $(INSTALL_DIR)/bin
-@@ -122,9 +128,10 @@
+@@ -122,9 +128,10 @@ 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 +137,7 @@ 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 @@
+@@ -134,7 +141,7 @@ endif
 
 deinstall:
 	rm -f $(INSTALL_DIR)/bin/ffindex_get $(INSTALL_DIR)/bin/ffindex_build $(INSTALL_DIR)/bin/ffindex_modify \

--- a/debian/patches/basename.patch
+++ b/debian/patches/basename.patch
@@ -10,7 +10,7 @@ Forwarded: yes

 --- a/src/ffindex_build.c
 +++ b/src/ffindex_build.c
-@@ -41,6 +41,8 @@ void usage(char *program_name)
+@@ -42,6 +42,8 @@ void usage(char *program_name)
                     "\t\t\tAnother append operations can be done without sorting.\n"
                     "\t-v\t\tprint version and other info then exit\n"
                     "\t-h\t\tdisplay this help message\n"
@@ -19,7 +19,7 @@ Forwarded: yes
                     "\nEXAMPLES:\n"
                     "\tCreate a new ffindex containing all files from the \"bar/\" directory containing\n"
                     "\tsay myfile1.txt, myfile2.txt and sort (-s) it so that e.g. ffindex_get can use it.\n"
-@@ -54,7 +56,7 @@ void usage(char *program_name)
+@@ -55,7 +57,7 @@ void usage(char *program_name)
                     "\tdefault maximum entries %d.\n"
                     "\tThis can be changed in the sources.\n"
                     FFINDEX_COPYRIGHT,
@@ -30,10 +30,10 @@ Forwarded: yes
 int main(int argn, char **argv)
 --- a/src/ffindex_from_fasta.c
 +++ b/src/ffindex_from_fasta.c
-@@ -33,8 +33,10 @@ void usage(char *program_name)
- {
-     fprintf(stderr, "USAGE: %s -v | [-s] data_filename index_filename fasta_filename\n"
-                     "\t-s\tsort index file\n"
+@@ -36,8 +36,10 @@ void usage(char *program_name)
+                     "\t-i\tuse identifier as name (you probably want -s too)\n"
+                     "\t-n\tuse incremental number as id (default)\n"
+                     "\t-v\tprint version\n"
 +                    "ENVIRONMENT\n"
 +                    "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
                     FFINDEX_COPYRIGHT,
@@ -42,7 +42,7 @@ Forwarded: yes
 }
 
 int main(int argn, char **argv)
-@@ -123,4 +125,4 @@ int main(int argn, char **argv)
+@@ -140,4 +142,4 @@ int main(int argn, char **argv)
   return err;
 }
 
@@ -94,7 +94,7 @@ Forwarded: yes
   }
 --- a/src/ffindex_get.c
 +++ b/src/ffindex_get.c
-@@ -28,8 +28,10 @@ void usage(char* program_name)
+@@ -29,8 +29,10 @@ void usage(char* program_name)
                     "\t-f FILE\t\tfile containing a list of file names, one per line\n"
                     "\t-h\t\tdisplay this help message\n"
                     "\t-n\t\tuse index of entry instead of entry name\n"

--- a/debian/patches/series
+++ b/debian/patches/series
-#Makefile.patch
-#basename.patch
-BuildSharedLibraryWithSameSuffix.patch
+Makefile.patch
+basename.patch