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NEWS
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NEWS
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Version 3.19
Thanks to Joemar Taggana, some incompatible utilities
were discovered in Mac OSX -- including incompatible
getopt and mktemp. Corrected confusion in tutorial
p. 3 regarding -m (Thanks to Erin Shellman). Corrected
spelling of ffpjsd option --hamann to --hamman.
Version 3.18
Rearranged ungetc character tests to come after
conversion of pipe to file. Fixed memory leak in
hash init(). Added support for large files (> 2GB) on 32
bit machines.
Version 3.17
Fixed bug in tempfile creation in function
convertPipeToFile().
Version 3.16
Fixed bug in ffpry with multiple headers parsed as a
single genome entry.
Version 3.15
Fixed bug in ffprwn.
Version 3.14
Added --disable-gui options to ./configure script. This
disables the perl based gui, so that the Perl/Tk module
isn't required for installation.
Version 3.13
Changed row terminal output for all programs from '\t\n'
(tab newline) to '\n' (newline) only. This makes output
from previous version incompatible with 3.13 but the
ffps can be easily converted using:
sed 's/\t$//' ffp > ffp.tmp ; mv ffp.tmp ffp
Version 3.12
Small bug fix for ffprwn for GNU compiler on 64 bit machines
where promotion of unsigned int to long unsigned int is
different. Thanks to Adrienne Breland at the University
of Nevada, Reno for finding this.
Version 3.10
Fixed minor bug in ffpry for fasta records pseudomolecule
input ENDING in NNNNNNNN, or other invalid characters.
Version 3.09
Fixed bug in ffpdf, related to initialized GROUP variable.
Updated license
Version 3.08
ffpgui
Added instructions to install a functional version of the
perl/tk module for using cygwin, in INSTALL.
Added error messages in ffpgui for running a vocab or
relative entropy profile without loading a file first.
Added additional sections to tutorial.pdf
Version 3.07
Added signal handling to all executables.
Broken pipes will cause a termination error in a pipeline
and will output 'PROGRAM: Broken pipe'
Expanded ./doc/tutorial.in.
Updated license.
Fixed inappropriate default -f setting (changed from 1 to
2) for ffpvprof.
Version 3.06
Added ffptree utility, which creates neighbor joining and
upgma trees. Date and version automatically updated
during build process.
Improved seeding of random generator when no seed is
provide via command line option: ffpry, ffpboot, ffpaa
Added processing via ffptree to ffpgui. The human
readable tree is displayed in the message window.
Started tutorial file in ./doc directory.
Added tutorial.pdf to doc directory
Version 3.05
Added length test since MAX_WORD_SIZE is 40: ffpry, ffpaa
ffpre.
Version 3.04
Added script ffpgui which is a Perl/Tk based GUI wrapper of
the various utilities.
Added --keys flag to ffpfilt to force keys to be output
instead of values only.
Version 3.03
Fixed overflow error with non-rabin karp hash used in ffpcol.
Version 3.02
The ffpaat utility has been removed from this package. The
purpose of this utility was to count amino acid features in
all nine frames from DNA fasta input. However obtaining
a proper translation of gene regions and using ffpaa is
generally more informative. This utility can still be
compiled and used from previous versions, but will not longer
be part of future releases.
Updated ffpre to Rabin-Karp hash, also fixed float overflow
errors and cases of nan, or inf in output. Text mode is now
implemented in ffpre.
Updated ffptxt to Rabin-Karp hash.
Version 3.01
Implementation of Rabin-Karp hash in ffpaa utility.
Similar speed gains as in ffpry obtained
ffpaa -l 20 NC_008253.faa
ffpaa (v.3.0) ----------- 9.35 s
ffpaa (v.3.01) ----------- 0.15 s
Input buffering options removed from both ffpaa and ffpry. The
optimal buffering size for the system is determined automatically
by using the stat.st_block size attribute of fstat or the compiler
default, whichever is greater. This is an effort to use the
filesystem's most efficient block size.
Upcoming v3.02 will include Rabin-Karp implementation of ffpre.
Version 3.0
Thanks to Nick Loman of University of Birmingham for pointing out
the cryptic nature of the "key-value" error messages when both
ffpfilt and ffpcol are used together in a pipeline successively.
All error messages from the utilities state the program issuing
the error.
Revamped tmpfile creation for non-seekable piped input, to use
most efficient buffering.
Added extra unit tests to confirm piped vs file argument output
is identical.
ffpry changes:
Beginning initial development of Rabin Karp Rolling hash function
implementations which has replaced the hashing function used
in version 2 in the ffpry executable. This has provided a
significant speedup in k-mer counting.
Here is a speed comparison:
ffpry -l 10 -d NC_008253.fna ------ 9.7s (v.3.0)
ffpry -l 10 -d NC_008253.fna ------ 1m28.2s (v.2.30
Removed all-possible/-a flag from ffpry. The only way to generate
columnar output from ffpry is via the -f flag and specify a specific
feature set.
-f specified features are now reverse complemented and classed as
is the input sequence by default.
Added -r option which disables reverse complementing of the input
sequence as well as operates on the feature list.
Fixed ffpry -f long option to correct value as per man file.
Other:
Fixed segmentation error in ffpboot
Future directions:
Rabin-Karp hash function will be implemented in ffpaa, ffptxt and
ffpre, ffpaat
Version 2.30
Fixed bug when encountering IUPAC codes in input files to ffpry.
Version 2.29
Fixed bug when piping input into ffpmerge.
Version 2.28
Addition of examples directory with trees from
Sims & Kim(2011) PNAS,108,8329-8334
BUGS: ffpre doesn't report errors for trying to open
non-existing second file arguments.
ffpre -l 5 loadfile -d
Version 2.27
ffpjsd: Added checks for overly long taxa names using the -p,
phylip 'infile' output option. Taxa names are now truncated to 10.
Version 2.26
Inclusion of ffpdf utility which finds clade 'distinguishing
features' as implemented in the paper Sims & Kim (2011), PNAS
Version 2.25
Major rewrite of ffpreprof and ffpvprof to support
piping in of files and TTY detection. Added
option for tmpfile directory specification in
ffpreprof and ffpvprof. Added -a,--amino option
to ffpvprof.
Added license header to the scripts
Version 2.23
Added LICENSE file
Added abilitity for C utilities to detect whether
the program is being run interactively or as part of
a pipeline. If a utility is run interactively with no
arguments then an errror message is spit out.
Made parsing of FNA and FAA files more robust, especially
when the files are formated strangely or there are many
characters which must be ignored because they are not
part of the alphabet set used by the utility.
In ffpaa and ffpry:
Added a non-fatal warning message that indicates that a
particular fna file has zero keys stored in output.
This usually indicates that the file is empty or contains
only characters which are not part of the alphabet set.
Version 2.22
Fixed ffpjsd -r bug. Previous output duplicated the diagonal.
Version 2.21
Fixed non-one diagonals in similarity matrix -s option
Added test of columnar/key-value input to ffpboot command
Version 2.20
Added Many new distance measures to ffpjsd
Version 2.19
Added manhattan distance and pearson correlation(R) similarity and 1-R-squared
distance calculation to ffpjsd.
Version 2.18
Updated manual files to include a few undocumented options and implemented
cosine distance calculation in ffpjsd.
Version 2.17
Added ffpcomplex to package. This is used to filter out high/low complexity features.
Version 2.16
Fixed -p bug in ffpjsd when specifying input file in argument list
Version 2.15
Completed ffpfilt utility.
Version 2.14
Added (key,value) test to ffprwn utility.
Version 2.11
Added the ffptxt utility which performs the ffp on 26 letter texts after removing non alphabetic
characters.
Version 2.10
Added ffpaat utility which translates nucleic acid sequence first into amino acid sequence and then
hashes the amino acid based features.
Version 2.09
Added -Multiple option to ffpry and ffpaa for processing of multiple sequences in one FNA/FAA file
Version 2.05
Enable long options in script files ffpvprof, ffpreprof and updated man files
Version 2.04
Enabled long options and updated all man files.
Version 2.03
ffpry option -d bug fixed. Now works with ATGC coding.
Version 2.02
ffpcol now read input properly from stdin
Added -a switch for amino acid sequences
ffpaa no longer seg faults on Red-hat Linux system
Added manpage for ffpcol, ffpcol.1