[med-svn] [fastx-toolkit] annotated tag upstream/0.0.14 created (now 109394c)
Andreas Tille
tille at debian.org
Sat Dec 10 08:37:50 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to annotated tag upstream/0.0.14
in repository fastx-toolkit.
at 109394c (tag)
tagging 17f6f4a0dad67b1b49ffbd7f2ad6206516cc24a1 (commit)
tagged by Andreas Tille
on Sat Dec 10 08:51:54 2016 +0100
- Log -----------------------------------------------------------------
Upstream version 0.0.14
A. Gordon (157):
First version in repository.
Added Galaxy-related files.
Removed Makefile.in files.
Test files for FASTA-Collapser tool.
Added <tests> to tools.
Added <help> and images to FASTX-Clipper tool.
Removed unneeded files from repository.
Added barcode-splitter tool.
Added 'script' sub-directory to the build process.
Added FASTQ-Nucleotides-Distribution tool.
Added FASTQ-Quality-Boxplot tool.
FASTQ-Statistics: move tip a bit higher in <help> section.
FASTQ-Boxplot-Quality - add script and XML tool.
Added FASTA-Clipping-Histgram tool.
Added <FASTX-Toolkit> comment in each XML file.
Applied Affero-GPLv3 license to all source files.
Changed 'modban' to 'adapter. Added Adapters tool-data file.
Changed the 'README' build-mess.
Added README, GALAXY-LICENSE.
Added Fasta-Collapser tool.
Added fastx_toolkit_conf.xml file.
Fixed toolkit path.
Changed sequence identifiers.
Updated README file with WARRANTY and installation instructions.
Added Galaxy semi-automatic installation script.
Added files to Makefile.am's.
Forked Galaxy XML tools into Regular and GZIP+Input.Tag versions.
Forgot to remove '$input.tag' from couple of tools.
Removed 'interpreter' from XML file - tool will use the global script.
Removed Solexa's modban from the tools XML file.
fixed wrong directory name.
Fixed missing entry in configure.ac.
Added missing files to EXTRA_DIST.
Prepared headers for CPP.
Added FASTX-Collapser tool.
FASTQ-Quality-Statistics now accepts FASTA files (not just FASTQ).
Renamed FASTQ-Quality-Stats to FASTX-Quality-Stats.
Fixed Makefile after FASTX-Quality-Stats rename.
Fixed compiler warnings about conflicting declarations.
Added max-count column to FASTX-Quality-Statistics.
Make fastq_nuc_dist_graph.sh DASH-compatible.
Change FASTQ-Qual-Stat to FASTX (in galaxy tools)
Renamed FASTA-Collapser to FASTX-Collapser.
Renamed FASTQ-Qual-Conv to FASTQ-Quality-Converter.
Renamed FASTA-Collapseri tool-id to FASTX-Collapser.
Renamed FASTQ-Qual-Stat to FASTX-Quality-Statistics.
Renamed FASTQ-Nuc-Dist to FASTX.
Fixed Makefiles, removed fasta_collapser.pl
Bumped version to 0.0.4
Added Sequence Alignment class to libfastx.
Added Local / HalfLocal sequence alignments.
Initial version of Alignment-based clipper.
Relatively good clipping results (compared to alex's clipper).
MFixed Major off-by-one bug (in all matrix calculations)
Somewhat stable version, good performace (compared to Alex's clipper).
2nd Gen FASTX-Clipper - RC1.
Enabled many errors and warning checks.
Tiny speed improvement - not resizing the matrix every round.
Use 'score_type' everywhere (instead of float/ssize_t)
Back to float, but still produces wrong results.
Fixed major bug introduced in rev 56 - forgot the reset match_matrix.
Re-written
Testing clipper improvments, v0.42.666.1
Fixed un-portable size_t in printf (for 64bit systems)
More printf portability
Shameful solution to an unexplained crash on CentOS 64bit.
fixed STUPID c/c++ memory bug - bumped version (and sent to Alex Dubin)
Improve error message with empty input.
Fixed static image path URL.
Bumped version, updated NEWS.
Added tag version-0.0.6 for changeset d3b688367f22
Removed tag version-0.0.6
Minor updates to usage information.
Added tag version-0.0.6 for changeset 988a160089cc
Added 'libgtextutils' dependency.
Added 'fasta-formatter'
Fixed old name types ( fasta_formatter was fasta_set_width )
Extracted sequence writers to separate header file.
EmptySequenceFilter uses pointer instead of reference + bugfix in
Bugfixes in MultiLine writer.
Added command line options and usage information.
Added AGPLv3 clauses
Minor bug - wrong line-number counting.
Added 'fasta_nucleotide_changer' ( RNA<->DNA / T<->U ) tool.
Added Galaxy tools and unit-testing for Fasta Formatter and nuc-changer tools.
Bumped version to 0.0.7, changed version string in usage information.
Fixed off-by-one bug.
Minor changes, to ease compilation on Mac OS X.
Removed unnecessary header.
Removed '-s $mismatches' options - not used in new clipper program.
Added tag Released as version 0.0.8 for changeset 856b121894a5
Bumped to version 0.0.9
FASTA-Clipping-Historgram - allow non-numeric sequence IDs + improved <help>
Added two new images to FASTA-Clipping-Histogram.
Now using the dynamic library libgtextutils (instead of static)
Bugfix: PATH_MAX conflicts on MacOS X.
New feature: support different offsets of FASTQ ASCII Quality scores.
new tool: fastx-renamer - based on idea & patch by Charles Plessy <plessy at riken.jp>
Barcode-Splitter: uses Galaxy's output.files_path to store multiple output
Fastx-Renamer: added galaxy's XML files.
Galaxy install script: copy the shell script, too.
libfastx: fix horrible bug: didn't actually validate the input nucleotides.
nucleotide-changer: allow U as input.
Bugfix: trimming too-short sequences causes segfault.
fastx.c: added sanity checks and input validation.
Fastx-Qual-Stat: added more details.
Added missing #include for printf()
New tool: FASTQ-Quality-Trimmer
Fastx-clipper: added <stdio.h> to avoid compilation problems.
Fastx-Collapser: removed (in)sanity check, preventing collapsing an
Fastx-Trimmer: added [-t] option to trim N bases from the end of the read.
new tool: fastx-uncollapser
fastx-collapser: allow re-collapsing of an already-collapsed FASTA file.
fastx-collapser: better verbose report.
merge fastx-recollapser branch
merge fasta-uncollapser
fastx-trimmer: fixed command-line parsing bug.
Fastq-Quality-Trimmer: updated usage string.
Fastx-Collapser: changed usage string and added verbose report.
Added XML files for new tools.
Updated sample tool_conf.xml
Added missing XML file.
Bumped version 0.0.11
Minor fixes to avoid compiler warnings on OpenSolaris
Fix compilation error on OpenSolaris
Bumped version to 0.0.12, but not final release yet.
Added LT_LDFLAGS and --enable-all-static option to ./configure
merge with static-binaries
Added ".hgignore" list
XML & Shell scripts updated, for better galaxy integration
Renamed the CSHL custom XML directory.
Allow quality scores to go higher than 40, upto 93
fastx-clipper: add -M option: minimum adapter alignment length.
Updated '.hgignore'
Changed location/files of CSHL-custom XML files.
Fixed 'configure.ac' with STD:TR1, config.h.in, etc.
Added a nice warning about missing 'std::tr1' for older compilers.
switched back to 'default' branch.
Added input validaion for quality-boxplot and nucleotide-distribution.
New tool: fastq_masker.
xml bug: wrong tool in fastq_quality_trimmer
Added 'fastq_masker' to ignore list
fastq_masker: added galaxy XML file.
added 'fastq_masker' to tool_conf.
XML files: use "-Q 33" or "-Q 64" based on input file.
XML files: fixed bugs/typos.
Makefile.am: added missing shell script for nuc-dist-line-graph.
Added input validation to 'nuc-dist-line-graph' shell script.
XML updates: minor changes to make Public and CSHL versions easier to compare.
More XML changes: make CUSTOM vs CSHL vesion even more similar.
Added/Updated functional tests for almost all the tools
Filename type: fastx instead of fastq (quality_trimmer)
Makefile.am typo for fastq_quality_trimmer
Hacked STD::TR1 check for missing files on CentOS 5.4
Bumped version to 0.0.13, added build-scripts, hacked m4 STD::TR1 detection.
Merge pull request #2 from Debian/typo
Bumped version to 0.0.14
Andreas Tille (1):
New upstream version 0.0.14
Assaf Gordon (14):
Maint: remove auto-generated files, add gitignore
Maint: improve autotools files
Added missing header, fix compilation issues.
gitignore: add INSTALL
BREAKING-CHANGE: default quality is now Sanger(33)
Updated Copyright year and contact email.
BREAKING-CHANGE: disallow empty nucleotide strings.
bugfix: invalid nucleotides were not properly detected.
Removed custom CSHL custom Galaxy XML files.
build: fix include path for 'make distcheck'.
build: remove unneeded file from configure.ac
configure.ac: bugfix for CXXFLAGS
fastx: improve ugly 'fgets' hack to avoid compilation warnings.
build: detect TR1 or C++11 with automake macros.
Charles Plessy (1):
Corrected a typo.
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