[med-svn] [hinge] 03/04: Merge tag 'upstream/0.42'

[Afif Elghraoui]

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commit 2de45eccd9852856fe8a1174b4064986b4f93a04
Merge: 3e4bb18 e62bdef
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon May 22 21:50:41 2017 -0400

    Merge tag 'upstream/0.42'
    
    Upstream version 0.42

 .gitignore                                         |    1 +
 .travis.yml                                        |   17 +-
 CMakeLists.txt                                     |   10 +-
 README.md                                          |   60 +-
 demo/NCTC9657_demo/run.sh                          |   37 +-
 demo/ecoli_P4_demo/run.sh                          |   40 +
 demo/ecoli_demo/run.sh                             |   29 +-
 demo/ecoli_demo/run_norevcomp.sh                   |   40 +
 demo/ecoli_nanopore/run.sh                         |   41 +
 demo/yeast_W303_demo/nominal.ini                   |   33 +
 demo/yeast_W303_demo/run.sh                        |   42 +
 docker/README.md                                   |    3 +-
 LICENSE => licence.txt                             |    2 +-
 misc/param_description1.png                        |  Bin 0 -> 10988 bytes
 parameter_description.md                           |   78 ++
 scripts/add_groundtruth.py                         |    0
 scripts/condense_graph.py                          |    0
 scripts/condense_graph_and_annotate.py             |    0
 scripts/condense_graph_annotate_clip_ends.py       |    0
 scripts/condense_graph_create_gfa_compute_n50.py   |    0
 scripts/condense_graph_with_gt.py                  |    0
 scripts/create_hgraph.py                           |    0
 scripts/draw_pileup_region_find_bridges.py         |  158 +++
 scripts/fasta_to_fastq.py                          |   20 +
 scripts/get_draft_path.py                          |  692 +++++-----
 scripts/get_draft_path_norevcomp.py                |  516 +-------
 scripts/get_single_strand.py                       |   16 +
 scripts/merge_hinges.py                            |    0
 scripts/pipeline_consensus.py                      |    0
 scripts/pipeline_consensus_norevcomp.py            |    0
 scripts/pipeline_nctc.py                           |    0
 scripts/pruning_and_clipping.py                    |  375 ++++--
 ...ipping2.py => pruning_and_clipping_nanopore.py} |  231 ++--
 scripts/random_condensation.py                     |    0
 scripts/repeat_annotate_reads.py                   |    0
 scripts/split_las.py                               |   21 +
 src/CMakeLists.txt                                 |   17 +
 src/consensus/CMakeLists.txt                       |    3 +-
 src/consensus/consensus.cpp                        |  104 +-
 src/consensus/draft.cpp                            | 1361 +++++++++++---------
 src/consensus/draft_chopper.cpp                    |   24 +-
 src/filter/CMakeLists.txt                          |    2 +
 src/filter/filter.cpp                              |  287 ++---
 src/hinge                                          |   58 +
 src/hinge.1.md                                     |   46 +
 src/include/LAInterface.h                          |   32 +-
 src/layout/CMakeLists.txt                          |    2 +
 src/layout/hinging.cpp                             |  717 ++++++-----
 src/lib/LAInterface.cpp                            |  393 ++++--
 src/maximal/CMakeLists.txt                         |    6 +
 src/maximal/maximal.cpp                            |  860 +++++++++++++
 utils/build.sh                                     |    3 +-
 utils/setup.sh                                     |    7 +-
 53 files changed, 3945 insertions(+), 2439 deletions(-)

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