[med-svn] [transdecoder] 01/02: Merge tag 'upstream/3.0.0+dfsg'

[Michael Crusoe]

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misterc-guest pushed a commit to tag debian/3.0.0+dfsg-1
in repository transdecoder.

commit cd6230978df7913e531d44b9c0a4a7107be1d1b1
Merge: 9f60ceb f9ac657
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Wed May 18 02:31:05 2016 -0700

    Merge tag 'upstream/3.0.0+dfsg'
    
    Upstream version 3.0.0+dfsg

 .gitmodules                                        |   3 +
 PerlLib/Gene_obj.pm                                |  20 +++
 TransDecoder.LongOrfs                              |  81 +++++++--
 TransDecoder.Predict                               |  99 ++++++++---
 notes                                              |   3 +
 sample_data/Makefile                               |  14 ++
 sample_data/cufflinks_example/Makefile             |   6 +
 sample_data/cufflinks_example/blastp.outfmt6.gz    | Bin 0 -> 1957 bytes
 .../cufflinks_example/blastp.results.outfmt6.gz    | Bin 1808 -> 0 bytes
 sample_data/cufflinks_example/cleanme.pl           |   7 +-
 sample_data/cufflinks_example/pfam.domtblout.gz    | Bin 12838 -> 12460 bytes
 sample_data/cufflinks_example/runMe.sh             |  41 +++--
 sample_data/pasa_example/Makefile                  |   6 +
 sample_data/pasa_example/cleanme.pl                |   2 +
 sample_data/pasa_example/pasa_assemblies.fasta.gz  | Bin 304896 -> 304706 bytes
 sample_data/pasa_example/pasa_assemblies.gff3.gz   | Bin 55455 -> 55467 bytes
 .../pasa_example/pasa_assemblies_described.txt.gz  | Bin 0 -> 231156 bytes
 sample_data/pasa_example/runMe.sh                  |  17 +-
 sample_data/simple_transcriptome_target/Makefile   |   6 +
 sample_data/simple_transcriptome_target/cleanme.pl |   1 +
 sample_data/simple_transcriptome_target/runMe.sh   |   4 +-
 util/cdna_alignment_orf_to_genome_orf.pl           |  62 ++++---
 util/remove_eclipsed_ORFs.pl                       |   4 +-
 util/single_best_ORF_per_transcript.pl             | 187 +++++++++++++++++++++
 24 files changed, 472 insertions(+), 91 deletions(-)

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