[med-svn] [trinityrnaseq] 03/04: Merge tag 'upstream/2.0.4+dfsg'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 16 07:10:16 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository trinityrnaseq.
commit 5e949542c79b1bffcabb3e91fa1b373daa5bba11
Merge: 2d19c7a a0eedbe
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Mon Feb 16 01:02:55 2015 -0500
Merge tag 'upstream/2.0.4+dfsg'
Upstream version 2.0.4+dfsg
Analysis/DifferentialExpression/run_DE_analysis.pl | 11 +-
Butterfly/Butterfly.jar | Bin 1427334 -> 0 bytes
Butterfly/prev_vers/Butterfly_r2013_08_14.jar | Bin 1150829 -> 0 bytes
Butterfly/src/src/jaligner/Alignment.java | 692 ---
Butterfly/src/src/jaligner/Cell.java | 98 -
Butterfly/src/src/jaligner/Directions.java | 44 -
Butterfly/src/src/jaligner/Markups.java | 47 -
Butterfly/src/src/jaligner/NeedlemanWunsch.java | 304 --
.../src/src/jaligner/NeedlemanWunschGotoh.java | 432 --
Butterfly/src/src/jaligner/Sequence.java | 250 --
Butterfly/src/src/jaligner/SmithWatermanGotoh.java | 388 --
Butterfly/src/src/jaligner/TracebackNode.java | 99 -
.../jaligner/example/NeedlemanWunschExample.java | 74 -
.../example/NeedlemanWunschGotohExample.java | 76 -
.../example/SmithWatermanGotohExample.java | 112 -
Butterfly/src/src/jaligner/example/package.html | 8 -
.../src/jaligner/example/sequences/p53_human.fasta | 7 -
.../src/jaligner/example/sequences/p53_mouse.fasta | 8 -
Butterfly/src/src/jaligner/formats/CLUSTAL.java | 121 -
Butterfly/src/src/jaligner/formats/FASTA.java | 79 -
Butterfly/src/src/jaligner/formats/Format.java | 59 -
.../src/src/jaligner/formats/FormatFactory.java | 84 -
Butterfly/src/src/jaligner/formats/Pair.java | 191 -
Butterfly/src/src/jaligner/formats/package.html | 8 -
.../src/src/jaligner/matrix/MatricesCompartor.java | 68 -
Butterfly/src/src/jaligner/matrix/Matrix.java | 80 -
.../src/src/jaligner/matrix/MatrixGenerator.java | 61 -
.../src/src/jaligner/matrix/MatrixLoader.java | 243 -
.../src/jaligner/matrix/MatrixLoaderException.java | 39 -
.../src/src/jaligner/matrix/matrices/BLOSUM100 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM30 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM35 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM40 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM45 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM50 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM55 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM60 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM62 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM65 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM70 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM75 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM80 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM85 | 31 -
.../src/src/jaligner/matrix/matrices/BLOSUM90 | 31 -
Butterfly/src/src/jaligner/matrix/matrices/BLOSUMN | 31 -
Butterfly/src/src/jaligner/matrix/matrices/DAYHOFF | 32 -
.../src/src/jaligner/matrix/matrices/EDNAFULL | 25 -
Butterfly/src/src/jaligner/matrix/matrices/GONNET | 26 -
.../src/src/jaligner/matrix/matrices/IDENTITY | 25 -
Butterfly/src/src/jaligner/matrix/matrices/MATCH | 25 -
Butterfly/src/src/jaligner/matrix/matrices/PAM10 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM100 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM110 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM120 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM130 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM140 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM150 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM160 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM170 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM180 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM190 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM20 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM200 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM210 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM220 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM230 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM240 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM250 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM260 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM270 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM280 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM290 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM30 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM300 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM310 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM320 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM330 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM340 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM350 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM360 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM370 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM380 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM390 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM40 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM400 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM410 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM420 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM430 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM440 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM450 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM460 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM470 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM480 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM490 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM50 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM500 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM60 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM70 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM80 | 34 -
Butterfly/src/src/jaligner/matrix/matrices/PAM90 | 34 -
Butterfly/src/src/jaligner/matrix/package.html | 8 -
Butterfly/src/src/jaligner/package.html | 8 -
.../jaligner/test/NeedlemanWunschGotohTester.java | 131 -
.../src/jaligner/test/NeedlemanWunschTester.java | 129 -
.../src/jaligner/test/RandomSequenceGenerator.java | 77 -
.../jaligner/test/SmithWatermanGotohTester.java | 131 -
Butterfly/src/src/jaligner/test/package.html | 8 -
.../jaligner/ui/filechooser/NamedInputStream.java | 67 -
Butterfly/src/src/jaligner/util/Commons.java | 222 -
.../src/src/jaligner/util/SequenceParser.java | 215 -
.../src/jaligner/util/SequenceParserException.java | 38 -
Butterfly/src/src/jaligner/util/package.html | 8 -
Makefile | 4 +-
Release.Notes | 10 +-
Trinity | 72 +-
sample_data/test_Trinity_Assembly/Makefile | 10 +-
.../__test_runMe_with_jaccard_clip.sh | 6 -
sample_data/test_Trinity_Assembly/cleanme.pl | 2 +
.../misc_run_tests/__runMe_with_qual_trimming.sh | 2 +-
...__runMe_with_qual_trimming_and_normalization.sh | 2 +-
.../__test_runMe_include_normalization.sh | 2 +-
.../__test_runMe_with_jaccard_clip.sh | 2 +-
trinity-plugins/GAL_0.2.1/README | 6 -
trinity-plugins/GAL_0.2.1/fasta_tool | 1053 -----
trinity-plugins/Makefile | 4 +-
trinity-plugins/TransDecoder_r20140704.tar.gz | Bin 21189681 -> 0 bytes
trinity-plugins/Trimmomatic-0.32/LICENSE | 674 ---
.../Trimmomatic-0.32/adapters/NexteraPE-PE.fa | 12 -
.../Trimmomatic-0.32/adapters/TruSeq2-PE.fa | 16 -
.../Trimmomatic-0.32/adapters/TruSeq2-SE.fa | 6 -
.../Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa | 12 -
.../Trimmomatic-0.32/adapters/TruSeq3-PE.fa | 4 -
.../Trimmomatic-0.32/adapters/TruSeq3-SE.fa | 4 -
.../Trimmomatic-0.32/trimmomatic-0.32.jar | Bin 118310 -> 0 bytes
trinity-plugins/Trimmomatic-0.32/trimmomatic.jar | 1 -
trinity-plugins/collectl/Tests.py | 117 -
trinity-plugins/collectl/build_collectl.sh | 53 -
trinity-plugins/collectl/collectl-3.6.9.src.tar.gz | Bin 467637 -> 0 bytes
trinity-plugins/collectl/collectl-3.7.4.src.tar.gz | Bin 462752 -> 0 bytes
trinity-plugins/collectl/make_data_files.py | 181 -
trinity-plugins/collectl/plot.py | 176 -
trinity-plugins/collectl/timetable.py | 33 -
trinity-plugins/parafly-code/LICENSE | 17 -
trinity-plugins/parafly-code/Makefile.am | 1 -
trinity-plugins/parafly-code/Makefile.in | 671 ---
trinity-plugins/parafly-code/aclocal.m4 | 951 ----
trinity-plugins/parafly-code/config.h | 23 -
trinity-plugins/parafly-code/config.h.in | 22 -
trinity-plugins/parafly-code/configure | 4685 --------------------
trinity-plugins/parafly-code/configure.ac | 15 -
trinity-plugins/parafly-code/depcomp | 688 ---
trinity-plugins/parafly-code/install-sh | 527 ---
trinity-plugins/parafly-code/missing | 331 --
trinity-plugins/parafly-code/src/Makefile.am | 6 -
trinity-plugins/parafly-code/src/Makefile.in | 449 --
trinity-plugins/parafly-code/src/ParaFly.cpp | 268 --
trinity-plugins/parafly-code/src/argProcessor.cpp | 61 -
trinity-plugins/parafly-code/src/argProcessor.hpp | 31 -
trinity-plugins/parafly-code/stamp-h1 | 1 -
trinity-plugins/rsem-1.2.19.tar.gz | Bin 9367568 -> 0 bytes
trinity-plugins/slclust/Makefile.bak | 10 +
util/align_and_estimate_abundance.pl | 8 +-
.../process_GMAP_alignments_gff3_chimeras_ok.pl | 3 +-
util/misc/run_GSNAP.pl | 51 +-
util/support_scripts/tests.py | 40 +-
165 files changed, 162 insertions(+), 18215 deletions(-)
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