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Revision history for Pairfq
Version Date Location
0.17.0 03/07/2017 Vancouver, BC
- Bug fix for handling opened processes. When the input is a named pipes or piped processes
through process substitution, these processes are now opened correctly.
- Bug fix for handling options to main program. The help/man/version options were not being
processed in the right order and were being treated as subcommands. Added an explicit
test for this behaviour and version information is now logged to the console during testing.
0.16.1 12/09/2016 Vancouver, BC
- Modify how options are processed in main application. Remove manual setting of
keys in option hash.
0.16.0 07/24/2016 Vancouver, BC
- Clean up Unix paths correctly (e.g. '/some/relative/../path' becomes '/some/path').
Fixes #10 on github.
0.15.0 12/22/2015 Vancouver, BC
- Major change in how compressing output is performed. Now, the data is piped directly
to the compression program so it is much more efficient that writing twice and deleting
the original data.
- The minor improvements with the new compression mechanism is that the file extension is
handled correctly, and there are fewer Perl dependencies since the compression is done
externally.
0.14.7 11/18/2015 Vancouver, BC
- Fix bug in compression method (syntax error with imported method).
0.14.6 10/03/2015 Vancouver, BC
- Use dispatch tables in main application for looking up methods and usage.
This makes adding methods easier and reduces the problem of checking input
for every command.
0.14.5 08/08/2015 Vancouver, BC
- Allow build system to find Perl instead of using environment
variables which may not work on all systems.
0.14.4 06/10/2015 Vancouver, BC
- Add option to write to STDOUT for 'addinfo' and 'joinpairs'
commands.
- Allow to read from stdin with a '-' or case-insensitive 'stdin'
term (this unintentionally only worked with uppercase STDIN before).
0.14.3 05/11/2015 Vancouver, BC
- Add conditional to check if comment is missing after pair
id with Illumina 1.8+ identifiers.
0.14.2 04/18/2015 Vancouver, BC
- Fix logging script name when reading from stdin.
0.14.1 11/18/2014 Vancouver, BC
- Remove dependencies used only for testing (List::MoreUtils
and IPC::System::Simple) in favor of core modules/methods.
0.14 10/27/2014 Vancouver, BC
- Replace BerkeleyDB indexing method with SQLite. This
makes installation much easier and doesn't require sudo to
install C libraries. This method also scales much better with
large data sets (e.g., speed up of about 50X for more than
10 million reads).
0.13.2 10/13/2014 Vancouver, BC
- Fix bug in 'pairfq_lite.pl' script. For some reason,
a temp file was being created for storage but it wasn't
being used. This was likely from a previous indexing method.
This did not affect any of the methods, it was just leaving
behind a temp file.
0.13.1 8/15/2014 Vancouver, BC
- Add DOI to make repo citable.
0.13 8/11/2014 Vancouver, BC
- Add method for finding pairs from an interleaved file
to main application and standalone script.
0.12 6/3/2014 Athens, GA
- Add method to not load modules until they are required.
- Remove List::Util dependency from main application.
0.11 4/14/2014 Athens, GA
- Bug fix for reading files containing a dash.
A patch was kindly provided by Dietmar Rieder.
0.10 3/20/2014 Athens, GA
-Add standalone script with no dependencies
or version requirements in a separate /scripts
directory.
- Improve doc readability by not listing path to program.
- Modify standalone script to work with v5.6 by
removing List::Util dep that is in not core in v5.6
(List::Util is in core in v5.8.9).
- Fix help message option listings for main application
and standalone script.
0.09.1 3/18/2014 Athens, GA
- Add check for ExtUtils::MakeMaker version.
- Remove tying objects for dbm files since we are no
longer filtering keys/values.
0.09 2/20/2014 Athens, GA
- Rework mk_key and mk_vec functions for storing data
so they do not use UTF-8 characters. This results in
a 40% decrease in execution time, and a 14% decrease
in memory usage for the default in memory execution.
- The indexing method now uses 185X less memory. This appears
to be due to a leak in the DB filter. The indexing method
is also 25% faster now.
- Due to removing the utf8 pragma, the version requirement has
now been lowered from 5.12 to 5.10.
- Make printing stats for 'makepairs' method an option.
0.08 2/10/2014 Athens, GA
- Bugfix for encoding read names with a comment line. Data
was not being decoded and this was causing no pairs to
be found.
- Update README to point to wiki instead of having lengthy
descriptions of each method in a single file.
0.07 1/27/2014 Athens, GA
- Remove use of DB_File. Reasons: 1) I discovered it has
only been a core module since v5.16 (I think, at least it was
not in v5.14.2). 2) It is much, much slower than BerkeleyDB and
less powerful in terms of features.
- This was the source of much frustration and failure trying to get
everything to work in cases where DB_File was present, or BerkeleyDB
was present, or neither. The best solution was simply to install
BerkeleyDB during the build process and forget about using DB_File
because it is quite slow and may not be available anyway (as I'd
assumed since I as using v5.18 -- and that's what the Perl docs describe).
0.06 1/25/2014 Athens, GA
- Added support for using BerkeleyDB if it is available,
but falling back to using DB_File for indexing method.
0.05 1/22/2014 Athens, GA
- Enhancements: 1) Make in-memory processing default instead of
optional. This should be the expected behavior and is most used,
so is a better default.
2) Make --index an option instead of this being the default.
This makes the code much more expressive now by checking if the
index option is defined, instead of seeing if the memory option
is not defined.
3) Add explicit exit or return from subroutines so it is clear
to anyone wanting to contribute what the flow of execution is
for each method.
4) More sig handlers for indexing method to clean up index.
0.04 11/18/2013 Athens, GA
- Bug fix for taking positional arguments (options were not
being recognized correctly). Add option to get version, for
testing or general use.
0.03 11/18/2013 Athens, GA
- Bug fixes for splitting pairs, storing files in memory,
and naming DBM files. Update/add tests.
0.02 11/11/2013 Athens, GA
- Removed all utility scripts and rolled methods into a single
executable. Completely redesigned pairfq to work as an application
with numerous methods, instead of a single script for just pairing
reads.
- Make individual methods positional arguments instead of options. Fix
formatting of output and add time/version stamp.
0.01 11/01/2013 Athens, GA
- Initial release.