[med-svn] [falcon] branch upstream updated (58a5f32 -> 67b5061)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository falcon.

      from  58a5f32   Imported Upstream version 1.8.3
       new  54d9a95   Imported Upstream version 1.8.4
       new  67b5061   Imported Upstream version 1.8.4

The 2 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/LAmerge.c                                 |   2 +-
 DAZZ_DB/GNUmakefile                                |   2 +-
 FALCON/falcon_kit/mains/get_read_ctg_map.py        |  12 +-
 FALCON/falcon_kit/mains/run1.py                    |  50 +-
 pypeFLOW/LICENSE => FALCON_unzip/LICENSE.txt       |   2 +-
 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/__init__.py                       |   0
 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/phased_ovlp_to_graph.py           | 515 ++++++++--------
 FALCON_unzip/falcon_unzip/phasing.py               | 569 +++++++++++++++++
 FALCON_unzip/falcon_unzip/phasing_readmap.py       |  73 +++
 .../falcon_unzip/rr_hctg_track.py                  |  66 +-
 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 +
 .../src/py_scripts/fc_dedup_h_tigs.py              |   3 +-
 .../src/py_scripts/fc_get_read_hctg_map.py         |   3 +-
 .../src/py_scripts/fc_graphs_to_h_tigs.py          |   3 +-
 .../src/py_scripts/fc_ovlp_filter_with_phase.py    |   5 +-
 .../src/py_scripts/fc_phased_ovlp_to_graph.py      |   4 +-
 .../src/py_scripts/fc_phasing.py                   |   4 +-
 .../src/py_scripts/fc_phasing_readmap.py           |   3 +-
 .../src/py_scripts/fc_quiver.py                    |   3 +-
 .../src/py_scripts/fc_rr_hctg_track.py             |   3 +-
 .../src/py_scripts/fc_select_reads_from_bam.py     |   3 +-
 .../src/py_scripts/fc_track_reads_htigs0.py        | 398 ++++++++++++
 .../src/py_scripts/fc_unzip.py                     |   3 +-
 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 +
 pypeFLOW/pwatcher/fs_based.py                      |   2 +-
 pypeFLOW/pwatcher/network_based.py                 |   2 +-
 pypeFLOW/pypeflow/simple_pwatcher_bridge.py        |  10 +-
 41 files changed, 3676 insertions(+), 352 deletions(-)
 copy pypeFLOW/LICENSE => FALCON_unzip/LICENSE.txt (97%)
 create mode 100644 FALCON_unzip/README.md
 create mode 100644 FALCON_unzip/examples/fc_unzip.cfg
 create mode 100644 FALCON_unzip/examples/unzip.sh
 create mode 100644 FALCON_unzip/examples/unzip_obsoleted.sh
 copy FALCON-make/LICENSE => FALCON_unzip/falcon_unzip/__init__.py (100%)
 create mode 100644 FALCON_unzip/falcon_unzip/dedup_h_tigs.py
 create mode 100644 FALCON_unzip/falcon_unzip/get_read_hctg_map.py
 create mode 100644 FALCON_unzip/falcon_unzip/graphs_to_h_tigs.py
 create mode 100644 FALCON_unzip/falcon_unzip/ovlp_filter_with_phase.py
 copy FALCON/falcon_kit/mains/ovlp_to_graph.py => FALCON_unzip/falcon_unzip/phased_ovlp_to_graph.py (90%)
 create mode 100644 FALCON_unzip/falcon_unzip/phasing.py
 create mode 100644 FALCON_unzip/falcon_unzip/phasing_readmap.py
 copy FALCON/falcon_kit/mains/rr_ctg_track.py => FALCON_unzip/falcon_unzip/rr_hctg_track.py (71%)
 create mode 100644 FALCON_unzip/falcon_unzip/run_quiver.py
 create mode 100644 FALCON_unzip/falcon_unzip/select_reads_from_bam.py
 create mode 100644 FALCON_unzip/falcon_unzip/unzip.py
 create mode 100755 FALCON_unzip/setup.py
 copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_dedup_h_tigs.py (57%)
 copy FALCON/src/py_scripts/fc_ovlp_stats.py => FALCON_unzip/src/py_scripts/fc_get_read_hctg_map.py (54%)
 copy FALCON/src/py_scripts/fc_ovlp_stats.py => FALCON_unzip/src/py_scripts/fc_graphs_to_h_tigs.py (54%)
 copy FALCON/src/py_scripts/fc_ctg_link_analysis.py => FALCON_unzip/src/py_scripts/fc_ovlp_filter_with_phase.py (51%)
 copy FALCON/src/py_scripts/fc_dedup_a_tigs.py => FALCON_unzip/src/py_scripts/fc_phased_ovlp_to_graph.py (53%)
 copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_phasing.py (59%)
 copy FALCON/src/py_scripts/fc_ovlp_stats.py => FALCON_unzip/src/py_scripts/fc_phasing_readmap.py (55%)
 copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_quiver.py (58%)
 copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_rr_hctg_track.py (56%)
 copy FALCON/src/py_scripts/fc_actg_coordinate.py => FALCON_unzip/src/py_scripts/fc_select_reads_from_bam.py (52%)
 create mode 100644 FALCON_unzip/src/py_scripts/fc_track_reads_htigs0.py
 copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_unzip.py (58%)
 create mode 100644 FALCON_unzip/src/py_utils/align.sh
 create mode 100644 FALCON_unzip/src/py_utils/call_SV_from_mum.py
 create mode 100644 FALCON_unzip/src/py_utils/fetch_read.py
 create mode 100644 FALCON_unzip/src/py_utils/split_bam.py

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