[med-svn] [ariba] branch upstream updated (e3b0c67 -> 110e4fe)

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

satta pushed a change to branch upstream
in repository ariba.

      from  e3b0c67   New upstream version 2.10.3+ds
       new  110e4fe   New upstream version 2.11.0+ds

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:
 README.md                                          | 122 ++++++++++---
 ariba/assembly.py                                  | 114 +++++++++++-
 ariba/cluster.py                                   |  95 +++++++---
 ariba/clusters.py                                  | 199 +++++++++++++--------
 ariba/common.py                                    |  10 +-
 ariba/external_progs.py                            |  16 +-
 ariba/mic_plotter.py                               |   2 +
 ariba/tasks/run.py                                 |   4 +-
 ariba/tests/assembly_test.py                       |  48 ++++-
 ariba/tests/cluster_test.py                        |  72 +++++---
 ...mbly_test_assemble_with_spades_fails_reads_1.fq |   4 +
 ...mbly_test_assemble_with_spades_fails_reads_2.fq |   5 +
 ... assembly_test_assemble_with_spades_reads_1.fq} |   0
 ... assembly_test_assemble_with_spades_reads_2.fq} |   0
 .../assembly_test_check_spades_log_file.log.bad    |   5 +
 .../assembly_test_check_spades_log_file.log.good   |   5 +
 scripts/ariba                                      |   6 +
 setup.py                                           |   2 +-
 18 files changed, 548 insertions(+), 161 deletions(-)
 create mode 100644 ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq
 create mode 100644 ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq
 copy ariba/tests/data/{assembly_assemble_with_fermilite.reads_1.fq => assembly_test_assemble_with_spades_reads_1.fq} (100%)
 copy ariba/tests/data/{assembly_assemble_with_fermilite.reads_2.fq => assembly_test_assemble_with_spades_reads_2.fq} (100%)
 create mode 100644 ariba/tests/data/assembly_test_check_spades_log_file.log.bad
 create mode 100644 ariba/tests/data/assembly_test_check_spades_log_file.log.good

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