[med-svn] [transdecoder] branch upstream updated (9d2e299 -> f9ac657)

[Michael Crusoe]

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misterc-guest pushed a change to branch upstream
in repository transdecoder.

      from  9d2e299   Imported Upstream version 2.1.0+dfsg
      adds  f9ac657   Imported Upstream version 3.0.0+dfsg

No new revisions were added by this update.

Summary of changes:
 .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(-)
 create mode 100644 .gitmodules
 create mode 100644 sample_data/Makefile
 create mode 100644 sample_data/cufflinks_example/Makefile
 create mode 100644 sample_data/cufflinks_example/blastp.outfmt6.gz
 delete mode 100644 sample_data/cufflinks_example/blastp.results.outfmt6.gz
 create mode 100644 sample_data/pasa_example/Makefile
 create mode 100644 sample_data/pasa_example/pasa_assemblies_described.txt.gz
 create mode 100644 sample_data/simple_transcriptome_target/Makefile
 create mode 100755 util/single_best_ORF_per_transcript.pl

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