File: RELEASE_NOTES

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ffindex 0.9.9.9-2
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For updated version, please see public git log.


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