.dockerignore

+.git/
+.idea/
+bin/
+build/
+test/
+cmake-build-debug/
+cmake-build-release/

.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

.hgignore

-.*\.o
-test_big
-bin
-lib
-include

.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
+
+
+

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)
+

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/

LICENSE

 AUTHOR
 
-FFindex was designed and implemented by Andreas Hauser <andy@splashground.de>.
+FFindex was designed and implemented by Andreas Hauser <hauser@genzentrum.lmu.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, excempt ffutil.h and ffutil.c which are also available
-under MIT license.
+parts of this work.
 
 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:

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" 

README → README.md

-* Copyright
+# 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>.
 
-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).
@@ -9,85 +21,86 @@ which basically captures the spirit of the Gnu Public License (GPL).
 See:
 http://creativecommons.org/licenses/by-sa/3.0/
 
-* Thanks
+[ ![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 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
 
-$ cd src
-$ make
-$ make test
+## Installation
 
-If you have MPI and want to compile ffindex_apply_mpi:
-$ make HAVE_MPI=1
+### Compilation
+With the sourcecode ready, simply run cmake with the default settings and libraries should be auto-detected:
 
-On OS X use for the first make line:
-$ make -f Makefile.osx
+	mkdir build
+	cd build
+	cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=${INSTALL_BASE_DIR} ..
+	make
+	make install
 
-# Please use a sensible value for INSTALL_DIR, e.g. /usr/local or /opt/ffindex
-# or $HOME/ffindex instead of "..".
-$ make install INSTALL_DIR=.. 
 
-and with MPI:
+**Please use a sensible value for ${INSTALL_BASE_DIR}, e.g. /usr/local or /opt/ffindex or $HOME/ffindex**
 
-$ make install INSTALL_DIR=.. HAVE_MPI=1
 
-
-* Usage
+### Setting environment variables
 
 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="$INSTALL_DIR/bin:$PATH"
-$ export LD_LIBRARY_PATH="$INSTALL_DIR/lib:$LD_LIBRARY_PATH"
+
+	export PATH="${INSTALL_BASE_DIR}/bin:${PATH}"
+	export LD_LIBRARY_PATH="${INSTALL_BASE_DIR}/lib:${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 -d out-wc.ffdata -- wc -c
+
+	mpirun -np 4 ffindex_apply_mpi fasta.ffdata fasta.ffindex -i out-wc.ffindex -o out-wc.ffdata -- wc -c

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

VERSION

-0.9.9.7
+0.9.9

debian/changelog

+ffindex (0.9.9.7+soedinglab+git20180802-1) unstable; urgency=medium
+
+  * Team upload.
+
+  * New upstream source to help compile hhsuite 3
+  * Removed 'get-orig-source' debian/rules target
+  * Introduction of 'basename' does not apply and should go through
+    upstream - skipped
+  * Removed any notion of _tsv binary that do not seem
+    available upstream.
+
+ -- Steffen moeller <moeller@debian.org>  Thu, 02 Aug 2018 18:45:59 +0200
+
 ffindex (0.9.9.7-4) unstable; urgency=medium
 
   * Team upload

debian/control

@@ -9,9 +9,9 @@ Build-Depends: debhelper (>= 10),
                libopenmpi-dev,
                openmpi-bin,
                chrpath
-Standards-Version: 4.0.0
-Vcs-Browser: https://anonscm.debian.org/git/debian-med/ffindex.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/ffindex.git
+Standards-Version: 4.2.0
+Vcs-Browser: https://salsa.debian.org/med-team/ffindex.git
+Vcs-Git: https://salsa.debian.org/med-team/ffindex.git
 Homepage: http://www.splashground.de/~andy/programs/FFindex/
 
 Package: ffindex

debian/docs

-README
+README.md

debian/libffindex0-dev.install

 usr/include/*
 usr/lib/libffindex.a
 usr/lib/libffindex.so
-src/ffindex_posix_search.h usr/include
+# not found
+#src/ffindex_posix_search.h usr/include

debian/patches/BuildSharedLibraryWithSameSuffix.patch

+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
+ )
+ 
+ 

debian/patches/series

-Makefile.patch
-basename.patch
+#Makefile.patch
+#basename.patch
+BuildSharedLibraryWithSameSuffix.patch

debian/rules

@@ -17,7 +17,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 %:
 	dh $@
 
-FFMANPAGES = ffindex_apply.1 ffindex_build.1 ffindex_from_fasta.1 ffindex_get.1 ffindex_modify.1 ffindex_unpack.1 ffindex_apply_mpi.1 ffindex_from_tsv.1
+FFMANPAGES = ffindex_apply.1 ffindex_build.1 ffindex_from_fasta.1 ffindex_get.1 ffindex_modify.1 ffindex_unpack.1
+#FFMANPAGES += ffindex_from_tsv.1
 ffmanpages: $(FFMANPAGES)
 BINNAMES =	\
 		ffindex_apply="apply a program to each FFindex entry";\
@@ -26,18 +27,21 @@ BINNAMES =	\
 		ffindex_get="retrieve entries from file index";\
 		ffindex_modify="modify file index entries";\
 		ffindex_unpack="unpack file index entries";\
-		ffindex_apply_mpi="apply a program to each FFindex entry (mpi enhanced)";\
 		ffindex_from_tsv="populate index from TSV file";
 
+# MPI binaries built when openmpi headers+library installed
+FFMANPAGES += ffindex_apply_mpi.1
+BINNAMES   += ffindex_apply_mpi="apply a program to each FFindex entry (mpi enhanced)";
+
 override_dh_installman: $(FFMANPAGES)
 	dh_installman
 
 $(FFMANPAGES): %.1 : debian/tmp/usr/bin/%
 	unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && eval '$(BINNAMES)' && help2man --no-info --no-discard-stderr '--help-option= ' -n "$$$*" --version-option="-v" '$<' -o '$@' --include debian/man_notes.nroff
 
-override_dh_clean:
-	rm -f $(FFMANPAGES)
-	dh_clean
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -rf $(FFMANPAGES) CMakeFiles ext CMakeCache.txt
 
 override_dh_install:
 	dh_install
@@ -48,10 +52,6 @@ override_dh_install:
 override_dh_auto_test:
 	dh_auto_test -- FFINDEX_MAX_INDEX_ENTRIES=20000 check
 
-get-orig-source:
-	mkdir -p ../tarballs
-	uscan --verbose --force-download --destdir=../tarballs
-
 override_dh_installexamples:
 	dh_installexamples
 	cp -aR test $(sampledir)/;

debian/watch

-version=3
+version=4
 
-# Homepage  Pattern  [Version  [Action]]
-http://www.splashground.de/~andy/programs/FFindex/ \
-	ffindex-([0-9][0-9.]*)\.tar\.[gzbl2]{2,3}
+# Formerly, does not have ffsort_index
+# # Homepage  Pattern  [Version  [Action]]
+# http://www.splashground.de/~andy/programs/FFindex/ \
+# 	ffindex-([0-9][0-9.]*)\.tar\.[gzbl2]{2,3}
+
+https://github.com/soedinglab/ffindex_soedinglab
+
+# GitHub hosted projects
+opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%ffindex-$1.tar.gz%" \
+   https://github.com/soedinglab/ffindex_soedinglab/tags \
+   (?:.*?/)?v?(\d[\d.]*)\.tar\.gz debian uupdate

perl5/FFindex.pm

-#
-# A simple perl native Module interfacing FFindex
-# written by Andreas Hauser <andreas-source@creative-memory.de
-#
-
-package FFindex;
-
-use Sys::Mmap;
-
-sub new
-{
-    my $class = shift;
-    my $self = {
-        ffdata_filename   => shift,
-        ffindex_filename  => shift,
-        mode              => shift,
-        ffdata            => undef,
-        ffdata_file       => undef,
-        ffindex_file      => undef,
-        ffindex           => [],
-        ffindex_hash      => {},
-        n_entries         => []
-    };
-
-    bless $self, $class;
-
-    #new Sys::Mmap $self->{ffdata}, 0, $self->{ffdata_filename} or die $!;
-    open($self->{ffdata_file}, "<", $self->{ffdata_filename});
-    mmap($self->{ffdata}, 0, PROT_READ, MAP_SHARED, $self->{ffdata_file}) or die $!;
-    open($self->{ffindex_file}, "<", $self->{ffindex_filename});
-
-    my $fh = $self->{ffindex_file};
-    my $i = 0;
-    while( my $line = <$fh>)
-    {   
-      chomp $line;
-      my ($name, $offset, $len) = split(/\t/, $line);
-      $self->{ffindex}[$i] = [$name, $offset, $len];
-      $self->{ffindex_hash}{$name} = $self->{ffindex}[$i];
-      $i++;
-    }
-    $self->{n_entries} = $i;
-
-    return $self;
-}
-
-
-sub get_num_entries()
-{
-  my( $self ) = @_;
-  return $self->{n_entries};
-}
-
-
-sub get_entry_by_index()
-{
-  my( $self, $index ) = @_;
-  return $self->{ffindex}[$index];
-}
-
-
-sub get_entry_by_name()
-{
-  my( $self, $qname ) = @_;
-  return $self->{ffindex_hash}{$qname};
-}
-
-
-sub get_data_by_index()
-{
-  my( $self, $index ) = @_;
-  my ($name, $offset, $len) = @{$self->{ffindex}[$index]};
-  return substr($self->{ffdata}, $offset, $len - 1);
-}
-
-
-sub get_data_by_name()
-{
-  my( $self, $qname ) = @_;
-  my ($name, $offset, $len) = @{$self->{ffindex_hash}{$qname}};
-  return substr($self->{ffdata}, $offset, $len - 1);
-}
-
-
-
-sub DESTROY
-{
-  close($self->{ffdata_file});
-  close($self->{ffindex_file});
-  $self->{ffindex} = undef;
-}
-
-
-1;