[med-svn] [pbalign] branch master updated (e37cb3e -> 3059f76)
Afif Elghraoui
afif at moszumanska.debian.org
Sat Dec 24 02:17:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository pbalign.
from e37cb3e Prepare for upload to unstable
new e530517 Imported Upstream version 0.3.0
new 3221648 Merge tag 'upstream/0.3.0'
new 914bcf1 Readability improvements and clean-ups in d/control and d/rules
new 59f9d8c Update email address and copyright year
new 5f1351c Bump Standards-Version to 3.9.8
new 4a6bd5c Use encrypted protocols for VCS URLs
new 3120bb9 Add build-dependency on pbcommand
new 3059f76 Prepare new revision
The 8 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 +-
debian/changelog | 11 +
debian/control | 73 ++--
debian/copyright | 2 +-
debian/rules | 5 +-
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 +-
75 files changed, 1892 insertions(+), 1339 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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