.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/README.source

+ffindex for Debian
+==================
+
+The official development of ffindex is discontinued.  However, a fork
+is maintained by
+
+    https://github.com/soedinglab/ffindex_soedinglab
+
+which is used in hhsuite.  Since the main focus of the Debian packaging
+is hhsuite[1] this fork is replacing the original code in the packaging.
+
+[1] https://lists.debian.org/debian-med/2019/01/msg00013.html
+
+ -- Andreas Tille <tille@debian.org>  Wed, 09 Jan 2019 11:37:23 +0100

debian/changelog

+ffindex (0.9.9.7.soedinglab+git20171201.74550c8-1) unstable; urgency=medium
+
+  * Revert latest change and base packaging again on soedinglab
+    (see README.source)
+  * Standards-Version: 4.3.0
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+
+ -- Andreas Tille <tille@debian.org>  Wed, 09 Jan 2019 16:45:16 +0100
+
 ffindex (0.9.9.7+sog+git20160415.14274c9-1) unstable; urgency=medium
 
   * The previous location on Github was an improperly chosen fork

debian/control

@@ -8,11 +8,12 @@ Build-Depends: debhelper (>= 11~),
                help2man,
                libopenmpi-dev,
                openmpi-bin,
+               cmake (>= 3.11),
                chrpath
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 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/
+Homepage: https://github.com/soedinglab/ffindex_soedinglab
 
 Package: ffindex
 Architecture: any

debian/libffindex0-dev.install

 usr/include/*
 usr/lib/libffindex.a
 usr/lib/libffindex.so
-src/ffindex_posix_search.h usr/include

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
+ )
+ 
+ 

debian/patches/Makefile.patch

-Description: Makefile fixes
-  * make Makefile DESTDIR-aware
-  * other changes to allow help2man to work better.
-  * deinstall -> uninstall
-  * pass CPPFLAGS and LDFLAGS for hardening
-  .
-  Upstream is aware but not interested in DESTDIR.
-Forwarded: yes
-Author: Laszlo Kajan <lkajan@debian.org>
-Author: Graham Inggs <ginggs@debian.org>
-Last-Update: 2017-06-29
-
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -1,17 +1,22 @@
--INSTALL_DIR?=..
--libdir=`([ -d /usr/lib64 ] && echo lib64) || echo lib`
-+PREFIX?=/usr
-+INSTALL_DIR=$(DESTDIR)$(PREFIX)
-+libdir=lib
- LANG=C
- #CC=musl-gcc
- #OMPI_CC=musl-gcc
- #CC=gcc
- #CC=icc
- #CC=clang
--CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I.
--LDFLAGS=-lffindex -L.
-+CFLAGS+=-std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. $(CPPFLAGS)
-+SOCURRENT=2
-+SOREVISION=0
-+SOAGE=2
-+SOVERSION=$(SOCURRENT).$(SOREVISION).$(SOAGE)
-+SOMAJORV=$(shell echo $$(( $(SOCURRENT)-$(SOAGE) )) )
- 
- OS:= $(shell uname)
- 
--FFINDEX_LIBS=libffindex.so libffindex.so.0.1 libffindex.a
-+FFINDEX_LIBS=libffindex.so libffindex.so.$(SOVERSION) libffindex.a
- 
- FFINDEX_HEADERS=ffindex.h ffindex_posix_search.h ffutil.h
- FFINDEX_OBJECTS=$(FFINDEX_HEADERS:.h=.o)
-@@ -34,30 +39,30 @@ libffindex.a: $(FFINDEX_OBJECTS)
- 	ar rcs libffindex.a $^
- 
- ifeq ($(OS), Darwin)
--libffindex.so.0.1: $(FFINDEX_OBJECTS) ext/fmemopen.o
--		$(CC) -shared -o libffindex.so.0.1 $^
-+libffindex.so.$(SOVERSION): $(FFINDEX_OBJECTS) ext/fmemopen.o
-+		$(CC) -shared -o libffindex.so.$(SOVERSION) $^
- else
- 
-  ifdef FFINDEX_STATIC
- STATIC=-static
-  endif
- 
--libffindex.so.0.1: $(FFINDEX_OBJECTS)
--		$(CC) -Wl,-z,defs -Wl,-soname,libffindex.so.0.1 -shared -o libffindex.so.0.1 $^
-+libffindex.so.$(SOVERSION): $(FFINDEX_OBJECTS)
-+		$(CC) $(LDFLAGS) -Wl,-z,defs -Wl,-soname,libffindex.so.$(SOVERSION) -shared -o libffindex.so.$(SOVERSION) $^
- 
- endif
- 
--libffindex.so: libffindex.so.0.1
--	ln -sf libffindex.so.0.1 libffindex.so
-+libffindex.so: libffindex.so.$(SOVERSION)
-+	ln -sf libffindex.so.$(SOVERSION) libffindex.so
- 
- ffindex_apply.o: ffindex_apply_mpi.c $(FFINDEX_LIBS)
- 	$(CC) $(CFLAGS) -c ffindex_apply_mpi.c -o $@ 
- 
- ffindex_apply: ffindex_apply.o $(FFINDEX_LIBS)
--	$(CC) $(CFLAGS) -o $@  ffindex_apply.o $(LDFLAGS) $(STATIC)
-+	$(CC) $(CFLAGS) -o $@  ffindex_apply.o $(LDFLAGS) -L. -lffindex
- 
- ffindex_apply_mpi: ffindex_apply_mpi.o $(FFINDEX_LIBS)
--	mpicc $(CFLAGS) -DHAVE_MPI -o $@  ffindex_apply_mpi.o $(LDFLAGS)
-+	mpicc $(CFLAGS) -DHAVE_MPI -o $@  ffindex_apply_mpi.o $(LDFLAGS) -L. -lffindex
- 
- 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 $(LDFLAGS) -L. -lffindex
- 
--test:
-+check:
- 	rm -f /tmp/test.data /tmp/test.ffindex
- 	LD_LIBRARY_PATH=".:$(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:
- 
- clean:
- 	rm -f $(FFINDEX_PROGRAMS) $(FFINDEX_OBJECTS) $(FFINDEX_LIBS) \
--		libffindex.so libffindex.so.0.1 libffindex.a \
-+		libffindex.so libffindex.so.$(SOVERSION) libffindex.a \
- 		ffindex_build.o ffindex_get.o ffindex_modify.o ffindex_from_fasta.o ffindex_apply_mpi.o \
--		ffindex_apply.o ffindex_from_tsv.o ffindex_unpack.o ffindex_posix_search.o ffindex_apply_mpi_spawn.o
-+		ffindex_apply.o ffindex_from_tsv.o ffindex_unpack.o ffindex_posix_search.o ffindex_apply_mpi_spawn.o \
-+		$(OBJECTS) $(OBJECTS:%=%.o)
- 
- install:
- 	mkdir -p $(INSTALL_DIR)/bin
-@@ -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
--	install libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so.0.1
-+	install libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOVERSION)
- 	install libffindex.a $(INSTALL_DIR)/$(libdir)/libffindex.a
--	ln -sf libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.so
-+	ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOMAJORV)
-+	ln -sf libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.so
- 	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
- 
- deinstall:
- 	rm -f $(INSTALL_DIR)/bin/ffindex_get $(INSTALL_DIR)/bin/ffindex_build $(INSTALL_DIR)/bin/ffindex_modify \
--		$(INSTALL_DIR)/$(libdir)/libffindex.so.0.1 $(INSTALL_DIR)/$(libdir)/libffindex.a \
-+		$(INSTALL_DIR)/$(libdir)/libffindex.so.$(SOVERSION) $(INSTALL_DIR)/$(libdir)/libffindex.a \
- 		$(INSTALL_DIR)/$(libdir)/libffindex.so $(INSTALL_DIR)/include/ffindex.h $(INSTALL_DIR)/include/ffutil.h\
- 		$(INSTALL_DIR)/include/ffindex_posix_search.h $(INSTALL_DIR)/bin/ffindex_from_fasta $(INSTALL_DIR)/bin/ffindex_from_tsv
- 	rmdir $(INSTALL_DIR)/bin || true

debian/patches/basename.patch

-Author: Laszlo Kajan <lkajan@rostlab.org>
-Author: Elso Andras <elso.andras@gmail.com>
-Subject: 40000000 bug and basename
- [Laszlo Kajan]
- The default value 40000000 for FFINDEX_MAX_INDEX_ENTRIES_DEFAULT is too high for a machine with 2G (or less) RAM.
- Bug fixed by introducing an environment variable FFINDEX_MAX_INDEX_ENTRIES to control the value.
- [Elso Andras]
- using basename for usage print, this helps help2man if a packager is using it
-Forwarded: yes
-
---- a/src/ffindex_build.c
-+++ b/src/ffindex_build.c
-@@ -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"
-+                    "ENVIRONMENT\n"
-+                    "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
-                     "\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"
-@@ -55,7 +57,7 @@ void usage(char *program_name)
-                     "\tdefault maximum entries %d.\n"
-                     "\tThis can be changed in the sources.\n"
-                     FFINDEX_COPYRIGHT,
--                    program_name, MAX_FILENAME_LIST_FILES, FFINDEX_MAX_ENTRY_NAME_LENTH, FFINDEX_MAX_INDEX_ENTRIES_DEFAULT);
-+                    basename(program_name), MAX_FILENAME_LIST_FILES, FFINDEX_MAX_ENTRY_NAME_LENTH, FFINDEX_MAX_INDEX_ENTRIES_DEFAULT);
- }
- 
- int main(int argn, char **argv)
---- a/src/ffindex_from_fasta.c
-+++ b/src/ffindex_from_fasta.c
-@@ -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,
--                    program_name);
-+                    basename(program_name));
- }
- 
- int main(int argn, char **argv)
-@@ -140,4 +142,4 @@ int main(int argn, char **argv)
-   return err;
- }
- 
--/* 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 0.997
- #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.
-+// lkajan: let the default remain 80000000, and let the actual value be controlled by the env var FFINDEX_MAX_INDEX_ENTRIES wherever FFINDEX_MAX_INDEX_ENTRIES_DEFAULT is used.
- #define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 80000000
- #define FFINDEX_MAX_ENTRY_NAME_LENTH 63
- 
-@@ -76,6 +78,8 @@ int ffindex_index_close(ffindex_index_t*
- /* return *out_data_file, *out_index_file, out_offset. */
- int ffindex_index_open(char *data_filename, char *index_filename, char* mode, FILE **out_data_file, FILE **out_index_file, size_t *out_offset);
- 
-+inline size_t ffindex_max_index_entries(){ char *FMIE = getenv("FFINDEX_MAX_INDEX_ENTRIES"); if( FMIE ) { return atol( FMIE ); } else { return FFINDEX_MAX_INDEX_ENTRIES_DEFAULT; } }
-+
- 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)
-                     "\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"
-+                    "ENVIRONMENT\n"
-+                    "\tFFINDEX_MAX_INDEX_ENTRIES - allocate memory for this number of entries\n"
-                     FFINDEX_COPYRIGHT,
--                    program_name);
-+                    basename(program_name));
- }
- 
- int main(int argn, char **argv)
---- a/src/ffindex_modify.c
-+++ b/src/ffindex_modify.c
-@@ -41,7 +41,7 @@ void usage(char *program_name)
-                     "\tTo clean up the data file after unlinking insert it to an new one:\n"
-                     "\tffindex_build -as cleaned.ffdata cleaned.ffindex -d foo.ffdata -i foo.ffindex\n"
-                     FFINDEX_COPYRIGHT,
--                    program_name, MAX_FILENAME_LIST_FILES, program_name);
-+                    basename(program_name), MAX_FILENAME_LIST_FILES, basename(program_name));
- }
- 
- int main(int argn, char **argv)
---- a/src/ffindex.c
-+++ b/src/ffindex.c
-@@ -373,7 +373,7 @@ ffindex_entry_t* ffindex_bsearch_get_ent
- ffindex_index_t* ffindex_index_parse(FILE *index_file, size_t num_max_entries)
- {
-   if(num_max_entries == 0)
--    num_max_entries = FFINDEX_MAX_INDEX_ENTRIES_DEFAULT;
-+    num_max_entries = ffindex_max_index_entries();
- 
-   size_t nbytes = sizeof(ffindex_index_t) + (sizeof(ffindex_entry_t) * num_max_entries);
-   ffindex_index_t *index = (ffindex_index_t *)mmap(0, nbytes, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0);

debian/patches/debug_segfault

+Description: Debugging code used for #907624
+
+--- a/src/ffindex.c
++++ b/src/ffindex.c
+@@ -165,6 +165,8 @@ int ffindex_insert_list_file(FILE *data_
+   char path[PATH_MAX];
+   while(fgets(path, PATH_MAX, list_file) != NULL) {
+     char *name = strdup(basename(path));
++    printf("DEBUG: %s (%i): name = %s\n", __FILE__, __LINE__, name);
++    fflush(stdout);
+     ffindex_insert_file(data_file, index_file, &offset, ffnchomp(path, strlen(path)), ffnchomp(name, strlen(name)));
+     free(name);
+   }
+@@ -322,6 +324,8 @@ ffindex_index_t* ffindex_index_parse(FIL
+   if(num_max_entries == 0)
+     num_max_entries = FFINDEX_MAX_INDEX_ENTRIES_DEFAULT;
+   size_t nbytes = sizeof(ffindex_index_t) + (sizeof(ffindex_entry_t) * num_max_entries);
++  printf("DEBUG: %s (%i): ffindex_index_parse(): nbytes = %li\n", __FILE__, __LINE__, nbytes);
++
+   ffindex_index_t *index = (ffindex_index_t *)malloc(nbytes);
+   if(index == NULL)
+   {
+@@ -350,9 +354,15 @@ ffindex_index_t* ffindex_index_parse(FIL
+   for(i = 0; d < (index->index_data + index->index_data_size); i++)
+   {
+     int p;
++    printf("DEBUG: %s (%i): ffindex_index_parse(): i=%li, d=%s, index->index_data=%li, index->index_data_size=%li\n", __FILE__, __LINE__, i, d, index->index_data, index->index_data_size);
+     for(p = 0; *d != '\t'; d++)
++{
++printf("DEBUG: %s (%i): ffindex_index_parse(): p=%i, *d=%c\n", __FILE__, __LINE__, p, *d);
+       index->entries[i].name[p++] = *d;
++}
+     index->entries[i].name[p] = '\0';
++    printf("DEBUG: %s (%i): ffindex_index_parse(): index->entries[%i].name = %s\n", __FILE__, __LINE__, i, index->entries[i].name);
++    fflush(stdout);
+     index->entries[i].offset = strtoull(d, &end, 10);
+     d = end;
+     index->entries[i].length  = strtoull(d, &end, 10);
+@@ -439,11 +449,15 @@ void ffindex_sort_index_file(ffindex_ind
+ int ffindex_write(ffindex_index_t* index, FILE* index_file)
+ {
+   /* Use tree if available */
++  printf("DEBUG: %s (%i): ffindex_write()\n", __FILE__, __LINE__);
++  fflush(stdout);
+   if(index->type == TREE)
+     return ffindex_tree_write(index, index_file);
+ 
+   for(size_t i = 0; i < index->n_entries; i++)
+   {
++    printf("DEBUG: %s (%i): ffindex_write(), i = %li\n", __FILE__, __LINE__, i);
++    fflush(stdout);
+     ffindex_entry_t ffindex_entry = index->entries[i];
+     if(fprintf(index_file, "%s\t%zd\t%zd\n", ffindex_entry.name, ffindex_entry.offset, ffindex_entry.length) < 0)
+       return EXIT_FAILURE;
+@@ -551,6 +565,32 @@ void action(const void *node, const VISI
+         case postorder:
+         case leaf:
+             entry = *(ffindex_entry_t **) node;
++            printf("DEBUG: %s(%i): %p\n", __FILE__, __LINE__, entry);
++            fflush(stdout);
++            if ( !entry ) {
++                fprintf(stderr, "No entry found in %s line %i\n", __FILE__, __LINE__-2);
++                break;
++            }
++            printf("DEBUG: %s(%i): before checking entry->offset\n", __FILE__, __LINE__);
++            fflush(stdout);
++            if ( !entry->offset ) {
++                fprintf(stderr, "Entry has no offset in %s line %i\n", __FILE__, __LINE__-10);
++                break;
++            } else {
++                printf("DEBUG: %s(%i): entry->offset = %li\n", __FILE__, __LINE__, entry->offset);
++            }
++            printf("DEBUG: %s(%i): before checking entry->name\n", __FILE__, __LINE__);
++            fflush(stdout);
++            if ( !entry->name ) {
++                fprintf(stderr, "Entry has no name in %s line %i\n", __FILE__, __LINE__-6);
++                break;
++            } else {
++                printf("DEBUG: %s(%i): entry->name = %s\n", __FILE__, __LINE__, entry->name);
++            }
++            printf("DEBUG: %s(%i): before printing both\n", __FILE__, __LINE__);
++            fflush(stdout);
++            printf("DEBUG: %s(%i): entry->name = %s, entry->offset = %li\n", __FILE__, __LINE__, entry->name, entry->offset);
++            fflush(stdout);
+             if(fprintf(index_file, "%s\t%zd\t%zd\n", entry->name, entry->offset, entry->length) < 0)
+                 break;
+     }
+@@ -560,7 +600,9 @@ int ffindex_tree_write(ffindex_index_t*
+ {
+   int ret = EXIT_SUCCESS;
+ 
++  printf("DEBUG: %s(%i): in ffindex_tree_write(): index = %p\n", __FILE__, __LINE__, index);
+   twalkmisc(index->tree_root, action, (void *) index_file);
++  printf("DEBUG: %s(%i): after twalkmisc in ffindex_tree_write()\n", __FILE__, __LINE__);
+   return ret;
+ }
+ 
+@@ -568,6 +610,8 @@ void ffsort_index(const char* index_file
+   FILE* index_fh = fopen(index_filename, "r");
+   size_t lines = ffcount_lines(index_filename);
+ 
++  printf("DEBUG: %s (%i): name = %s, lines = %li\n", __FILE__, __LINE__, index_filename, lines);
++  fflush(stdout);
+   ffindex_index_t* index = ffindex_index_parse(index_fh, lines);
+   fclose(index_fh);
+ 
+--- a/src/ffindex_modify.c
++++ b/src/ffindex_modify.c
+@@ -106,10 +106,14 @@ int main(int argn, char **argv)
+ 
+   index_file = fopen(index_filename, "r+");
+   if(index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
++  printf("DEBUG: %s (%i): index_file = %s\n", __FILE__, __LINE__, index_filename);
++  fflush(stdout);
+ 
+   size_t entries = ffcount_lines(index_filename);
+   ffindex_index_t* index = ffindex_index_parse(index_file, entries);
+   if(index == NULL) { perror("ffindex_index_parse failed"); return (EXIT_FAILURE); }
++  printf("DEBUG: %s (%i): index_file = %s, entries = %li\n", __FILE__, __LINE__, index_filename, entries);
++  fflush(stdout);
+ 
+   fclose(index_file);
+ 
+@@ -118,11 +122,14 @@ int main(int argn, char **argv)
+   {
+     if(use_tree)
+     {
++  printf("DEBUG: %s (%i): unlink + use_tree\n", __FILE__, __LINE__);
++
+       /* Build tree */
+       index = ffindex_index_as_tree(index);
+ 
+       /* For each list_file unlink all entries */
+       if(list_filenames_index > 0)
++  printf("DEBUG: %s (%i): list_filenames_index = %i\n", __FILE__, __LINE__, list_filenames_index);
+         for(int i = 0; i < list_filenames_index; i++)
+         {
+           printf("Unlinking entries from '%s'\n", list_filenames[i]);
+@@ -137,7 +144,10 @@ int main(int argn, char **argv)
+ 
+       /* unlink entries specified by args */
+       for(int i = optind; i < argn; i++)
++{
++  printf("DEBUG: %s (%i): i = %i\n", __FILE__, __LINE__, i);
+         index = ffindex_unlink(index, argv[i]);
++}
+     }
+     else
+     {
+@@ -178,8 +188,14 @@ int main(int argn, char **argv)
+ 
+   /* Write index back */
+   index_file = fopen(index_filename, "w");
++  printf("DEBUG: %s (%i): index_file = %s, entries = %li\n", __FILE__, __LINE__, index_filename, entries);
++  fflush(stdout);
++
+   if(index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
+   err += ffindex_write(index, index_file);
++  printf("DEBUG: %s (%i): err = %i\n", __FILE__, __LINE__, err);
++  fflush(stdout);
++
+   return err;
+ }
+ 

debian/patches/no_opt

+Description: Switch off optimisation - does not help
+
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -1,5 +1,5 @@
+ cmake_minimum_required(VERSION 3.11)
+-set(CMAKE_C_FLAGS "-std=c99 ${CMAKE_C_FLAGS}")
++set(CMAKE_C_FLAGS "-std=c99 -O0")
+ 
+ # sets HAVE_FMEMOPEN
+ add_subdirectory(ext)