[med-svn] [trinityrnaseq] branch upstream updated (1a1969d -> a0eedbe)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 16 07:10:21 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository trinityrnaseq.
from 1a1969d Imported Upstream version 2.0.3+dfsg
new a0eedbe Imported Upstream version 2.0.4+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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
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 +-
164 files changed, 152 insertions(+), 18215 deletions(-)
delete mode 100644 Butterfly/Butterfly.jar
delete mode 100644 Butterfly/prev_vers/Butterfly_r2013_08_14.jar
delete mode 100644 Butterfly/src/src/jaligner/Alignment.java
delete mode 100644 Butterfly/src/src/jaligner/Cell.java
delete mode 100644 Butterfly/src/src/jaligner/Directions.java
delete mode 100644 Butterfly/src/src/jaligner/Markups.java
delete mode 100644 Butterfly/src/src/jaligner/NeedlemanWunsch.java
delete mode 100644 Butterfly/src/src/jaligner/NeedlemanWunschGotoh.java
delete mode 100644 Butterfly/src/src/jaligner/Sequence.java
delete mode 100644 Butterfly/src/src/jaligner/SmithWatermanGotoh.java
delete mode 100644 Butterfly/src/src/jaligner/TracebackNode.java
delete mode 100644 Butterfly/src/src/jaligner/example/NeedlemanWunschExample.java
delete mode 100644 Butterfly/src/src/jaligner/example/NeedlemanWunschGotohExample.java
delete mode 100644 Butterfly/src/src/jaligner/example/SmithWatermanGotohExample.java
delete mode 100644 Butterfly/src/src/jaligner/example/package.html
delete mode 100644 Butterfly/src/src/jaligner/example/sequences/p53_human.fasta
delete mode 100644 Butterfly/src/src/jaligner/example/sequences/p53_mouse.fasta
delete mode 100644 Butterfly/src/src/jaligner/formats/CLUSTAL.java
delete mode 100644 Butterfly/src/src/jaligner/formats/FASTA.java
delete mode 100644 Butterfly/src/src/jaligner/formats/Format.java
delete mode 100644 Butterfly/src/src/jaligner/formats/FormatFactory.java
delete mode 100644 Butterfly/src/src/jaligner/formats/Pair.java
delete mode 100644 Butterfly/src/src/jaligner/formats/package.html
delete mode 100644 Butterfly/src/src/jaligner/matrix/MatricesCompartor.java
delete mode 100644 Butterfly/src/src/jaligner/matrix/Matrix.java
delete mode 100644 Butterfly/src/src/jaligner/matrix/MatrixGenerator.java
delete mode 100644 Butterfly/src/src/jaligner/matrix/MatrixLoader.java
delete mode 100644 Butterfly/src/src/jaligner/matrix/MatrixLoaderException.java
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM100
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM30
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM35
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM40
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM45
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM50
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delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM60
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM62
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM65
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM70
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delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM80
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM85
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUM90
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/BLOSUMN
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/DAYHOFF
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/EDNAFULL
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/GONNET
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/IDENTITY
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/MATCH
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM10
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM100
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM110
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM120
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM130
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM140
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM150
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM160
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM170
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM180
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM190
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM20
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM200
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM210
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM220
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM230
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM240
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM250
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM260
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM270
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM280
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM290
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM30
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM300
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM310
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM320
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM330
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM340
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM350
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM360
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM370
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM380
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM390
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM40
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM400
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM410
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM420
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM430
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM440
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM450
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM460
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM470
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM480
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM490
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM50
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM500
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM60
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM70
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM80
delete mode 100644 Butterfly/src/src/jaligner/matrix/matrices/PAM90
delete mode 100644 Butterfly/src/src/jaligner/matrix/package.html
delete mode 100644 Butterfly/src/src/jaligner/package.html
delete mode 100644 Butterfly/src/src/jaligner/test/NeedlemanWunschGotohTester.java
delete mode 100644 Butterfly/src/src/jaligner/test/NeedlemanWunschTester.java
delete mode 100644 Butterfly/src/src/jaligner/test/RandomSequenceGenerator.java
delete mode 100644 Butterfly/src/src/jaligner/test/SmithWatermanGotohTester.java
delete mode 100644 Butterfly/src/src/jaligner/test/package.html
delete mode 100644 Butterfly/src/src/jaligner/ui/filechooser/NamedInputStream.java
delete mode 100644 Butterfly/src/src/jaligner/util/Commons.java
delete mode 100644 Butterfly/src/src/jaligner/util/SequenceParser.java
delete mode 100644 Butterfly/src/src/jaligner/util/SequenceParserException.java
delete mode 100644 Butterfly/src/src/jaligner/util/package.html
delete mode 100755 sample_data/test_Trinity_Assembly/__test_runMe_with_jaccard_clip.sh
delete mode 100644 trinity-plugins/GAL_0.2.1/README
delete mode 100755 trinity-plugins/GAL_0.2.1/fasta_tool
delete mode 100644 trinity-plugins/TransDecoder_r20140704.tar.gz
delete mode 100644 trinity-plugins/Trimmomatic-0.32/LICENSE
delete mode 100644 trinity-plugins/Trimmomatic-0.32/adapters/NexteraPE-PE.fa
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delete mode 120000 trinity-plugins/Trimmomatic-0.32/trimmomatic.jar
delete mode 100755 trinity-plugins/collectl/Tests.py
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delete mode 100755 trinity-plugins/parafly-code/src/argProcessor.cpp
delete mode 100755 trinity-plugins/parafly-code/src/argProcessor.hpp
delete mode 100644 trinity-plugins/parafly-code/stamp-h1
delete mode 100644 trinity-plugins/rsem-1.2.19.tar.gz
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