[med-svn] [falcon] branch master updated (ccc50af -> d0a7449)

[Afif Elghraoui]

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afif pushed a change to branch master
in repository falcon.

      from  ccc50af   Update changelog
       new  215b426   Imported Upstream version 1.8.6
       new  b665960   Merge tag 'upstream/1.8.6'
       new  cd354e0   Remove copyright statements for removed sources
       new  d0a7449   Prepare new revision for 1.8.6 (tests still failing since 1.8.5)

The 4 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:
 FALCON/falcon_kit/bash.py                          |   36 +-
 FALCON/falcon_kit/functional.py                    |   14 +-
 FALCON/falcon_kit/mains/LAmerge.py                 |   51 +
 FALCON/falcon_kit/mains/LAsort.py                  |   46 +
 FALCON/falcon_kit/mains/run1.py                    |   14 +-
 FALCON/falcon_kit/pype_tasks.py                    |    8 +-
 FALCON/test/test_functional.py                     |    8 +
 FALCON_unzip/LICENSE.txt                           |   32 -
 FALCON_unzip/README.md                             |    1 -
 FALCON_unzip/examples/fc_unzip.cfg                 |   17 -
 FALCON_unzip/examples/unzip.sh                     |    2 -
 FALCON_unzip/examples/unzip_obsoleted.sh           |   33 -
 FALCON_unzip/falcon_unzip/__init__.py              |   36 -
 FALCON_unzip/falcon_unzip/dedup_h_tigs.py          |   70 -
 FALCON_unzip/falcon_unzip/get_read_hctg_map.py     |  110 --
 FALCON_unzip/falcon_unzip/graphs_to_h_tigs.py      |  678 ---------
 .../falcon_unzip/ovlp_filter_with_phase.py         |  354 -----
 FALCON_unzip/falcon_unzip/phased_ovlp_to_graph.py  | 1545 --------------------
 FALCON_unzip/falcon_unzip/phasing.py               |  570 --------
 FALCON_unzip/falcon_unzip/phasing_readmap.py       |   73 -
 FALCON_unzip/falcon_unzip/rr_hctg_track.py         |  201 ---
 FALCON_unzip/falcon_unzip/run_quiver.py            |  394 -----
 FALCON_unzip/falcon_unzip/select_reads_from_bam.py |  113 --
 FALCON_unzip/falcon_unzip/unzip.py                 |  357 -----
 FALCON_unzip/setup.py                              |   24 -
 FALCON_unzip/src/py_scripts/fc_dedup_h_tigs.py     |    4 -
 .../src/py_scripts/fc_get_read_hctg_map.py         |    4 -
 FALCON_unzip/src/py_scripts/fc_graphs_to_h_tigs.py |    4 -
 .../src/py_scripts/fc_ovlp_filter_with_phase.py    |    6 -
 .../src/py_scripts/fc_phased_ovlp_to_graph.py      |    5 -
 FALCON_unzip/src/py_scripts/fc_phasing.py          |    5 -
 FALCON_unzip/src/py_scripts/fc_phasing_readmap.py  |    4 -
 FALCON_unzip/src/py_scripts/fc_quiver.py           |    4 -
 FALCON_unzip/src/py_scripts/fc_rr_hctg_track.py    |    4 -
 .../src/py_scripts/fc_select_reads_from_bam.py     |    4 -
 .../src/py_scripts/fc_track_reads_htigs0.py        |  398 -----
 FALCON_unzip/src/py_scripts/fc_unzip.py            |    4 -
 FALCON_unzip/src/py_utils/align.sh                 |   10 -
 FALCON_unzip/src/py_utils/call_SV_from_mum.py      |   85 --
 FALCON_unzip/src/py_utils/fetch_read.py            |   12 -
 FALCON_unzip/src/py_utils/split_bam.py             |   28 -
 debian/changelog                                   |    6 +-
 debian/copyright                                   |    4 -
 pypeFLOW/pwatcher/fs_based.py                      |   30 +-
 pypeFLOW/pypeflow/do_task.py                       |    4 +
 pypeFLOW/pypeflow/simple_pwatcher_bridge.py        |   59 +-
 46 files changed, 232 insertions(+), 5239 deletions(-)
 create mode 100644 FALCON/falcon_kit/mains/LAmerge.py
 create mode 100644 FALCON/falcon_kit/mains/LAsort.py
 delete mode 100644 FALCON_unzip/LICENSE.txt
 delete mode 100644 FALCON_unzip/README.md
 delete mode 100644 FALCON_unzip/examples/fc_unzip.cfg
 delete mode 100644 FALCON_unzip/examples/unzip.sh
 delete mode 100644 FALCON_unzip/examples/unzip_obsoleted.sh
 delete mode 100644 FALCON_unzip/falcon_unzip/__init__.py
 delete mode 100644 FALCON_unzip/falcon_unzip/dedup_h_tigs.py
 delete mode 100644 FALCON_unzip/falcon_unzip/get_read_hctg_map.py
 delete mode 100644 FALCON_unzip/falcon_unzip/graphs_to_h_tigs.py
 delete mode 100644 FALCON_unzip/falcon_unzip/ovlp_filter_with_phase.py
 delete mode 100644 FALCON_unzip/falcon_unzip/phased_ovlp_to_graph.py
 delete mode 100644 FALCON_unzip/falcon_unzip/phasing.py
 delete mode 100644 FALCON_unzip/falcon_unzip/phasing_readmap.py
 delete mode 100644 FALCON_unzip/falcon_unzip/rr_hctg_track.py
 delete mode 100644 FALCON_unzip/falcon_unzip/run_quiver.py
 delete mode 100644 FALCON_unzip/falcon_unzip/select_reads_from_bam.py
 delete mode 100644 FALCON_unzip/falcon_unzip/unzip.py
 delete mode 100755 FALCON_unzip/setup.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_dedup_h_tigs.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_get_read_hctg_map.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_graphs_to_h_tigs.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_ovlp_filter_with_phase.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_phased_ovlp_to_graph.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_phasing.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_phasing_readmap.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_quiver.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_rr_hctg_track.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_select_reads_from_bam.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_track_reads_htigs0.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_unzip.py
 delete mode 100644 FALCON_unzip/src/py_utils/align.sh
 delete mode 100644 FALCON_unzip/src/py_utils/call_SV_from_mum.py
 delete mode 100644 FALCON_unzip/src/py_utils/fetch_read.py
 delete mode 100644 FALCON_unzip/src/py_utils/split_bam.py

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