[med-svn] [falcon] 03/06: Merge tag 'upstream/1.8.2'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository falcon.

commit 3ca0355517895beca2a91ba0843b7639da0c836b
Merge: b4e69f8 2a04b8e
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Nov 13 22:20:35 2016 -0800

    Merge tag 'upstream/1.8.2'
    
    Upstream version 1.8.2

 DALIGNER/LA4Falcon.c                               |  168 +-
 DAMASKER/tandem.c                                  |    2 +-
 DAZZ_DB/README                                     |   15 +-
 DAZZ_DB/fasta2DB.c                                 |    2 +
 DEXTRACTOR/DB.c                                    | 1736 +++++++++++++++++++
 DEXTRACTOR/DB.h                                    |  420 +++++
 DEXTRACTOR/GNUmakefile                             |   26 +
 DEXTRACTOR/LICENSE                                 |   34 +
 DEXTRACTOR/Makefile                                |   37 +
 DEXTRACTOR/QV.c                                    | 1387 ++++++++++++++++
 DEXTRACTOR/QV.h                                    |   96 ++
 DEXTRACTOR/README                                  |  141 ++
 DEXTRACTOR/dexqv.c                                 |  164 ++
 DEXTRACTOR/dexta.c                                 |  219 +++
 DEXTRACTOR/dextract.c                              |  594 +++++++
 DEXTRACTOR/undexqv.c                               |  230 +++
 DEXTRACTOR/undexta.c                               |  285 ++++
 FALCON-examples/git-sym.makefile                   |   10 +-
 FALCON-examples/makefile                           |    4 +-
 FALCON-examples/run/ecoli/input.fofn               |    6 +-
 FALCON-examples/run/ecoli/makefile                 |    4 +
 FALCON-examples/run/ecoli2/input.fofn              |    6 +-
 FALCON-examples/run/synth0/check.py                |    2 +-
 FALCON-examples/run/synth0/data/synth0.fasta       | 1750 --------------------
 FALCON-examples/run/synth0/data/synth5k/README     |    8 +
 .../run/synth0/data/{ => synth5k}/ref.fasta        |    0
 .../run/synth0/data/synth5k/subreads.dexta         |  Bin 0 -> 25665 bytes
 .../run/synth0/data/synth5k/synth5k.bam            |  Bin 0 -> 35341 bytes
 .../run/synth0/data/synth5k/synth5k.bam.bai        |  Bin 0 -> 16 bytes
 .../run/synth0/data/synth5k/synth5k.bam.pbi        |  Bin 0 -> 346 bytes
 .../run/synth0/data/synth5k/synth5k.xml            |   15 +
 FALCON-examples/run/synth0/fc_run.cfg              |   14 +-
 FALCON-examples/run/synth0/input.fofn              |    2 +-
 FALCON-make/makefile                               |    5 +-
 FALCON/falcon_kit/bash.py                          |   37 +-
 FALCON/falcon_kit/functional.py                    |   85 +-
 FALCON/falcon_kit/mains/ovlp_to_graph.py           |   35 +-
 FALCON/falcon_kit/mains/run0.py                    |  683 --------
 FALCON/falcon_kit/mains/run1.py                    |  738 ++++-----
 FALCON/falcon_kit/pype_tasks.py                    |  398 +++++
 FALCON/falcon_kit/run_support.py                   |   69 +-
 FALCON/falcon_kit/stats_preassembly.py             |    5 +-
 FALCON/setup.py                                    |    1 -
 FALCON/test/se161.sh                               |  836 ++++++++++
 FALCON/test/test_functional.py                     |   18 +-
 pypeFLOW/LICENSE                                   |   32 +
 pypeFLOW/License.txt                               |   20 -
 pypeFLOW/pwatcher/blocking.py                      |  464 ++++++
 pypeFLOW/pwatcher/fs_based.py                      |   60 +-
 pypeFLOW/pwatcher/mains/job_start.sh               |   36 +
 pypeFLOW/pwatcher/mains/network_heartbeat.py       |  176 ++
 pypeFLOW/pwatcher/mains/query_server.py            |  125 ++
 pypeFLOW/pwatcher/network_based.py                 | 1031 ++++++++++++
 pypeFLOW/pypeflow/do_support.py                    |   51 +
 pypeFLOW/pypeflow/do_task.py                       |  149 ++
 pypeFLOW/pypeflow/pwatcher_bridge.py               |   59 +-
 pypeFLOW/pypeflow/simple_pwatcher_bridge.py        |  566 +++++++
 pypeFLOW/pypeflow/util.py                          |   31 +
 pypeFLOW/setup.py                                  |    2 +
 pypeFLOW/travis.sh                                 |    2 +-
 60 files changed, 10053 insertions(+), 3038 deletions(-)

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