.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
-
-
-

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 <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:

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.md → README

-# 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

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
+0.9.9.8

debian/README.source

 ffindex for Debian
 ==================
 
-The official development of ffindex is discontinued.  However, a fork
-is maintained by
+There is a fork by soedinglab which is intended to support hhsuite.
+Unfortunately this fork had some code issues leading to SIGSEGV which
+is extensively documented in bug #907624.
 
-    https://github.com/soedinglab/ffindex_soedinglab
+The original author from ffindex wrote about this issue:
+
+  I do understand where the problem in the code is coming from.
+  They have a different way of working around the limitations
+  of the (broken) posix search interface.
+  .
+  They implemented a copy from the posix code  with what they needed
+  from the broken posix  interface.
+  .
+  In the meantime I solved the problem more elegantly, but they never
+  switched back.  They are now about 8 releases behind and have a
+  less good solution for their original problem.
+
+So it seems to be a good idea to stick to this version, specifically
+since the soedinglab fork is known to SIGSEGV.  The problem was, that
+the original ffindex 0.9.9.7 code did not provided the full interface
+used by hhsuite which is actually the main focus of the Debian Med
+team (see [1]).  Thus ffindex author released a new version:
+
+  I added the compatibility changes to ffindex and made a new release:
+  https://github.com/ahcm/ffindex/releases/tag/0.9.9.8
 
-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
 

debian/changelog

+ffindex (0.9.9.8-1) UNRELEASED; urgency=medium
+
+  * Revert again to original code which now added the interface for
+    hhsuite
+    Closes: #907624
+
+ -- Andreas Tille <tille@debian.org>  Fri, 11 Jan 2019 11:26:50 +0100
+
 ffindex (0.9.9.7.soedinglab+git20171201.74550c8-1) unstable; urgency=medium
 
   * Revert latest change and base packaging again on soedinglab

debian/control

@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
 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: https://github.com/soedinglab/ffindex_soedinglab
+Homepage: https://github.com/ahcm/ffindex
 
 Package: ffindex
 Architecture: any

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: ffindex
-Upstream-Contact: Andreas Hauser <andy@splashground.de>
-Source: http://www.splashground.de/~andy/programs/FFindex/
+Upstream-Contact: Andreas Hauser <andreas.cm@icloud.com>
+Source: https://github.com/ahcm/ffindex/releases
 
 Files: *
-Copyright: Andreas Hauser <andy@splashground.de>
+Copyright: 2010-2018 Andreas Hauser <andy@splashground.de>
 License: CC-BY-SA-3.0
 
 Files: src/ext/*
@@ -13,7 +13,7 @@ License: GPL-2.0+
 
 Files: debian/*
 Copyright: 2012-2013 Laszlo Kajan <lkajan@debian.org>
-           2014-2016 Andreas Tille <tille@debian.org>
+           2014-2018 Andreas Tille <tille@debian.org>
            2017 Graham Inggs <ginggs@debian.org>
 License: GPL-3.0+
 

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 0.998
+ #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)

debian/patches/series

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