[med-svn] [pbalign] branch upstream updated (b16dc6f -> e530517)
Afif Elghraoui
afif at moszumanska.debian.org
Sat Dec 24 02:17:07 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository pbalign.
from b16dc6f Imported Upstream version 0.2.0
new e530517 Imported Upstream version 0.3.0
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:
LICENSES.txt | 34 +-
Makefile | 11 +-
README.md | 18 +-
doc/howto.rst | 7 +-
pbalign/__init__.py | 4 +-
pbalign/alignservice/align.py | 6 +-
pbalign/alignservice/blasr.py | 105 ++++--
pbalign/bampostservice.py | 137 +++++++
pbalign/ccs.py | 32 ++
pbalign/filterservice.py | 33 +-
pbalign/forquiverservice/__init__.py | 34 --
pbalign/forquiverservice/forquiver.py | 99 -----
pbalign/forquiverservice/loadchemistry.py | 77 ----
pbalign/forquiverservice/loadpulses.py | 103 ------
pbalign/forquiverservice/repack.py | 87 -----
pbalign/forquiverservice/sort.py | 89 -----
pbalign/options.py | 416 ++++++++++++++--------
pbalign/pbalignfiles.py | 41 ++-
pbalign/pbalignrunner.py | 247 ++++++-------
pbalign/tasks/__init__.py | 0
pbalign/tasks/consolidate_alignments.py | 96 +++++
pbalign/tools/createChemistryHeader.py | 4 +-
pbalign/utils/fileutil.py | 35 +-
pbalign/utils/progutil.py | 2 +-
setup.py | 6 +-
tests/cram/bam.t | 14 +
tests/cram/ccs.t | 15 +
tests/cram/dataset_tiny.t | 38 ++
tests/cram/filtercriteria_hitpolicy.t | 78 ++++
tests/cram/path_with_space.t | 9 +
tests/cram/setup.sh | 21 ++
tests/cram/test_pbalign.t | 276 --------------
tests/cram/xml.t | 38 ++
tests/cram_h5/ccs.t | 51 +++
tests/cram_h5/filter_adapter_only.t | 11 +
tests/cram_h5/inputs_outputs.t | 130 +++++++
tests/cram_h5/pulsefile.t | 23 ++
tests/cram_h5/setup.sh | 22 ++
tests/{cram => cram_h5}/test_mask_aligned_reads.t | 2 +-
tests/data/1.config | 3 +-
tests/data/ecoli_lp.fofn | 4 +-
tests/data/lambda_bax.fofn | 2 +-
tests/data/reference_lambda.xml | 14 +
tests/data/subreads_dataset1.xml | 21 ++
tests/data/subreads_dataset2.xml | 10 +
tests/data/test_bas.fofn | 2 +-
tests/data/test_ccs.fofn | 2 +-
tests/data/test_filterAdapterOnly.fofn | 2 +-
tests/data/test_leftmost_query.fasta | 2 +-
tests/data/test_pulseFile.fofn | 8 +-
tests/out/readme | 3 +-
tests/unit/nose.cfg | 17 +
tests/unit/test_fileutil.py | 63 ++--
tests/unit/test_options.py | 109 +++---
tests/unit/test_pbalign.py | 37 +-
tests/unit/test_pbalignfiles.py | 31 +-
tests/unit/test_referenceInfo.py | 3 +-
tests/unit/test_setpath.py | 25 ++
tests/unit/test_tool_contract.py | 91 +++++
tests/unit/test_unrolled.py | 87 +++++
tests/unit/test_xmlout.py | 38 ++
tests/unit_h5/nose.cfg | 17 +
tests/{unit => unit_h5}/test_filterservice.py | 11 +-
tests/{unit => unit_h5}/test_forquiverservice.py | 11 +-
tests/{unit => unit_h5}/test_gmap.py | 8 +-
tests/{unit => unit_h5}/test_loadpulsesservice.py | 8 +-
tests/{unit => unit_h5}/test_pbalign.py | 11 +-
tests/{unit => unit_h5}/test_repackservice.py | 7 +-
tests/{unit => unit_h5}/test_rgnh5io.py | 10 +-
tests/unit_h5/test_setpath.py | 27 ++
tests/{unit => unit_h5}/test_sortservice.py | 5 +-
71 files changed, 1837 insertions(+), 1303 deletions(-)
create mode 100755 pbalign/bampostservice.py
create mode 100644 pbalign/ccs.py
delete mode 100755 pbalign/forquiverservice/__init__.py
delete mode 100755 pbalign/forquiverservice/forquiver.py
delete mode 100755 pbalign/forquiverservice/loadchemistry.py
delete mode 100755 pbalign/forquiverservice/loadpulses.py
delete mode 100755 pbalign/forquiverservice/repack.py
delete mode 100755 pbalign/forquiverservice/sort.py
create mode 100644 pbalign/tasks/__init__.py
create mode 100644 pbalign/tasks/consolidate_alignments.py
create mode 100644 tests/cram/bam.t
create mode 100644 tests/cram/ccs.t
create mode 100644 tests/cram/dataset_tiny.t
create mode 100644 tests/cram/filtercriteria_hitpolicy.t
create mode 100644 tests/cram/path_with_space.t
create mode 100755 tests/cram/setup.sh
delete mode 100644 tests/cram/test_pbalign.t
create mode 100644 tests/cram/xml.t
create mode 100644 tests/cram_h5/ccs.t
create mode 100644 tests/cram_h5/filter_adapter_only.t
create mode 100644 tests/cram_h5/inputs_outputs.t
create mode 100644 tests/cram_h5/pulsefile.t
create mode 100755 tests/cram_h5/setup.sh
rename tests/{cram => cram_h5}/test_mask_aligned_reads.t (96%)
create mode 100644 tests/data/reference_lambda.xml
create mode 100644 tests/data/subreads_dataset1.xml
create mode 100644 tests/data/subreads_dataset2.xml
create mode 100644 tests/unit/nose.cfg
create mode 100755 tests/unit/test_setpath.py
create mode 100755 tests/unit/test_tool_contract.py
create mode 100755 tests/unit/test_unrolled.py
create mode 100755 tests/unit/test_xmlout.py
create mode 100644 tests/unit_h5/nose.cfg
rename tests/{unit => unit_h5}/test_filterservice.py (85%)
rename tests/{unit => unit_h5}/test_forquiverservice.py (72%)
rename tests/{unit => unit_h5}/test_gmap.py (90%)
rename tests/{unit => unit_h5}/test_loadpulsesservice.py (73%)
copy tests/{unit => unit_h5}/test_pbalign.py (84%)
rename tests/{unit => unit_h5}/test_repackservice.py (72%)
rename tests/{unit => unit_h5}/test_rgnh5io.py (92%)
create mode 100755 tests/unit_h5/test_setpath.py
rename tests/{unit => unit_h5}/test_sortservice.py (84%)
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