[med-svn] [falcon] branch upstream updated (8bf7774 -> 2a04b8e)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository falcon.

      from  8bf7774   Imported Upstream version 1.7.5
       new  2a04b8e   Imported Upstream version 1.8.2

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:
 DALIGNER/LA4Falcon.c                               |  168 +-
 DAMASKER/tandem.c                                  |    2 +-
 DAZZ_DB/README                                     |   15 +-
 DAZZ_DB/fasta2DB.c                                 |    2 +
 {DAMASKER => DEXTRACTOR}/DB.c                      |    0
 {DAMASKER => DEXTRACTOR}/DB.h                      |    0
 {DAMASKER => DEXTRACTOR}/GNUmakefile               |   15 +-
 {DALIGNER => DEXTRACTOR}/LICENSE                   |    0
 DEXTRACTOR/Makefile                                |   37 +
 {DAMASKER => DEXTRACTOR}/QV.c                      |    0
 {DAMASKER => DEXTRACTOR}/QV.h                      |    0
 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, 6362 insertions(+), 3045 deletions(-)
 copy {DAMASKER => DEXTRACTOR}/DB.c (100%)
 copy {DAMASKER => DEXTRACTOR}/DB.h (100%)
 copy {DAMASKER => DEXTRACTOR}/GNUmakefile (62%)
 copy {DALIGNER => DEXTRACTOR}/LICENSE (100%)
 create mode 100644 DEXTRACTOR/Makefile
 copy {DAMASKER => DEXTRACTOR}/QV.c (100%)
 copy {DAMASKER => DEXTRACTOR}/QV.h (100%)
 create mode 100644 DEXTRACTOR/README
 create mode 100644 DEXTRACTOR/dexqv.c
 create mode 100644 DEXTRACTOR/dexta.c
 create mode 100644 DEXTRACTOR/dextract.c
 create mode 100644 DEXTRACTOR/undexqv.c
 create mode 100644 DEXTRACTOR/undexta.c
 create mode 100644 FALCON-examples/run/ecoli/makefile
 delete mode 100644 FALCON-examples/run/synth0/data/synth0.fasta
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/README
 rename FALCON-examples/run/synth0/data/{ => synth5k}/ref.fasta (100%)
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/subreads.dexta
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/synth5k.bam
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/synth5k.bam.bai
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/synth5k.bam.pbi
 create mode 100644 FALCON-examples/run/synth0/data/synth5k/synth5k.xml
 delete mode 100644 FALCON/falcon_kit/mains/run0.py
 create mode 100644 FALCON/falcon_kit/pype_tasks.py
 create mode 100644 FALCON/test/se161.sh
 create mode 100644 pypeFLOW/LICENSE
 delete mode 100644 pypeFLOW/License.txt
 create mode 100755 pypeFLOW/pwatcher/blocking.py
 create mode 100755 pypeFLOW/pwatcher/mains/job_start.sh
 create mode 100644 pypeFLOW/pwatcher/mains/network_heartbeat.py
 create mode 100755 pypeFLOW/pwatcher/mains/query_server.py
 create mode 100755 pypeFLOW/pwatcher/network_based.py
 create mode 100644 pypeFLOW/pypeflow/do_support.py
 create mode 100644 pypeFLOW/pypeflow/do_task.py
 create mode 100644 pypeFLOW/pypeflow/simple_pwatcher_bridge.py
 create mode 100644 pypeFLOW/pypeflow/util.py

-- 
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