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satta pushed a change to branch upstream
in repository ariba.
from 3ba4058 New upstream version 2.9.4+ds
new 5fd2631 New upstream version 2.10.0+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:
ariba/__init__.py | 1 +
ariba/flag.py | 3 ++
ariba/mic_plotter.py | 2 +-
ariba/ref_preparer.py | 8 ++++-
ariba/reference_data.py | 19 +++++++----
ariba/report_filter.py | 3 ++
ariba/report_flag_expander.py | 37 ++++++++++++++++++++++
ariba/tasks/__init__.py | 1 +
ariba/tasks/expandflag.py | 8 +++++
.../01.filter.check_genes.log | 10 +++---
.../data/reference_data_test_remove_bad_genes.log | 10 +++---
ariba/tests/data/report_flag_expander.run.in.tsv | 3 ++
ariba/tests/data/report_flag_expander.run.out.tsv | 3 ++
ariba/tests/flag_test.py | 8 +++++
ariba/tests/reference_data_test.py | 17 ++++++----
ariba/tests/report_filter_test.py | 15 +++++++++
ariba/tests/report_flag_expander_test.py | 20 ++++++++++++
scripts/ariba | 12 +++++++
setup.py | 2 +-
19 files changed, 157 insertions(+), 25 deletions(-)
create mode 100644 ariba/report_flag_expander.py
create mode 100644 ariba/tasks/expandflag.py
create mode 100644 ariba/tests/data/report_flag_expander.run.in.tsv
create mode 100644 ariba/tests/data/report_flag_expander.run.out.tsv
create mode 100644 ariba/tests/report_flag_expander_test.py
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