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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
khmer-2.1.2+dfsg/doc/dev/guidelines-continued-dev.rst-270-
khmer-2.1.2+dfsg/doc/dev/guidelines-continued-dev.rst:271: - [ ] the CPython object name is of the form `khmer_${OBJECTNAME}_Object`
khmer-2.1.2+dfsg/doc/dev/guidelines-continued-dev.rst-272- - [ ] Named struct with `PyObject_HEAD` macro
khmer-2.1.2+dfsg/doc/dev/guidelines-continued-dev.rst:273: - [ ] `static PyTypeObject khmer_${OBJECTNAME}_Type` with the following
khmer-2.1.2+dfsg/doc/dev/guidelines-continued-dev.rst-274- entries
##############################################
khmer-2.1.2+dfsg/doc/dev/guidelines-continued-dev.rst-296- - [ ] The reference count for the type object is incremented before adding
khmer-2.1.2+dfsg/doc/dev/guidelines-continued-dev.rst:297: it to the module: `Py_INCREF(&khmer_${OBJECTNAME}_Type);`.
##############################################
khmer-2.1.2+dfsg/doc/dev/release.rst-264-``git describe --tags --dirty --always``. This will be in the format
khmer-2.1.2+dfsg/doc/dev/release.rst:265:``${tagVersion}-${commits_ahead}-${revision_id}-${isDirty}``. Example:
khmer-2.1.2+dfsg/doc/dev/release.rst-266-``v0.6.1-18-g8a9e430-dirty``
##############################################
khmer-2.1.2+dfsg/doc/dev/release.rst-270-Lacking either of the two git-archive will record the version number at the top
khmer-2.1.2+dfsg/doc/dev/release.rst:271:of ``khmer/_version.py`` via the ``$Format:%d$`` and ``$Format:%H$``
khmer-2.1.2+dfsg/doc/dev/release.rst-272-placeholders enabled by the "export-subst" entry in ``.gitattributes``.
##############################################
khmer-2.1.2+dfsg/sandbox/streaming-assembly-simple.py-78- cg = create_countgraph(args)
khmer-2.1.2+dfsg/sandbox/streaming-assembly-simple.py:79: asm = khmer.JunctionCountAssembler(cg)
khmer-2.1.2+dfsg/sandbox/streaming-assembly-simple.py-80-
##############################################
khmer-2.1.2+dfsg/scripts/filter-abund-single.py-75- Trimmed sequences will be placed in
khmer-2.1.2+dfsg/scripts/filter-abund-single.py:76: ``${input_sequence_filename}.abundfilt``.
khmer-2.1.2+dfsg/scripts/filter-abund-single.py-77-
##############################################
khmer-2.1.2+dfsg/scripts/filter-abund.py-71- Trimmed sequences will be placed in
khmer-2.1.2+dfsg/scripts/filter-abund.py:72: ``${input_sequence_filename}.abundfilt`` for each input sequence file. If
khmer-2.1.2+dfsg/scripts/filter-abund.py-73- the input sequences are from RNAseq or metagenome sequencing then
##############################################
khmer-2.1.2+dfsg/scripts/merge-partitions.py-59- epilog = """\
khmer-2.1.2+dfsg/scripts/merge-partitions.py:60: Take the ``${graphbase}.subset.#.pmap`` files and merge them all into a
khmer-2.1.2+dfsg/scripts/merge-partitions.py:61: single ``${graphbase}.pmap.merged`` file for
khmer-2.1.2+dfsg/scripts/merge-partitions.py-62- :program:`annotate-partitions.py` to use.
##############################################
khmer-2.1.2+dfsg/scripts/partition-graph.py-69- epilog = """\
khmer-2.1.2+dfsg/scripts/partition-graph.py:70: The resulting partition maps are saved as ``${basename}.subset.#.pmap``
khmer-2.1.2+dfsg/scripts/partition-graph.py-71- files.
##############################################
khmer-2.1.2+dfsg/src/oxli/assembler.cc-183-{
khmer-2.1.2+dfsg/src/oxli/assembler.cc:184: linear_asm = new LinearAssembler(graph);
khmer-2.1.2+dfsg/src/oxli/assembler.cc-185-}
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-68- graph, contig = linear_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:69: asm = assembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-70-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-77- graph, contig = linear_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:78: asm = assembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-79-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-87- graph, contig = linear_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:88: asm = assembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-89-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-97- graph, contig = circular_linear_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:98: asm = assembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-99-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-114- graph, contig, L, HDN, R, tip = right_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:115: asm = khmer.LinearAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-116- path = asm.assemble(contig[0:K])
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-124- graph, contig, L, HDN, R, tip = right_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:125: asm = khmer.LinearAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-126- path = asm.assemble(revcomp(contig[0:K]))
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-133- graph, contig, L, HDN, R, tip = right_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:134: asm = khmer.LinearAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-135- path = asm.assemble(L)
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-142- graph, contig, L, HDN, R, tip = right_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:143: asm = khmer.LinearAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-144- path = asm.assemble(revcomp(L))
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-154- graph, contig, L, HDN, R, tip = right_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:155: asm = khmer.LinearAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-156- path = asm.assemble(R)
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-163- graph, contig, L, HDN, R, tip = right_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:164: asm = khmer.LinearAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-165- path = asm.assemble(contig[-K:])
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-181- graph, contig, L, HDN, R, tip = left_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:182: asm = khmer.LinearAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-183- path = asm.assemble(contig[-K:])
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-190- graph, contig, L, HDN, R, tip = left_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:191: asm = khmer.LinearAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-192- path = asm.assemble(HDN)
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-204-
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:205: asm = khmer.LinearAssembler(graph, stop_filter=stop_filter)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-206-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-218- stop_filter.count(tip)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:219: asm = khmer.LinearAssembler(graph, stop_filter=stop_filter)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-220-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-232- stop_filter.count(L) # ...and block original path
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:233: asm = khmer.LinearAssembler(graph, stop_filter=stop_filter)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-234-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-245- graph, contig, L, HDN, R, tip = left_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:246: asm = khmer.LinearAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-247-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-261- lh = khmer._GraphLabels(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:262: asm = khmer.SimpleLabeledAssembler(lh)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-263- hdn = graph.find_high_degree_nodes(contig)
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-278- lh = khmer._GraphLabels(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:279: asm = khmer.SimpleLabeledAssembler(lh)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-280-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-300- lh = khmer._GraphLabels(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:301: asm = khmer.SimpleLabeledAssembler(lh)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-302-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-324- lh = khmer._GraphLabels(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:325: asm = khmer.SimpleLabeledAssembler(lh)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-326-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-352- lh = khmer._GraphLabels(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:353: asm = khmer.SimpleLabeledAssembler(lh)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-354-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-367- lh = khmer._GraphLabels(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:368: asm = khmer.SimpleLabeledAssembler(lh)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-369-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-393- lh = khmer._GraphLabels(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:394: asm = khmer.SimpleLabeledAssembler(lh, stop_filter=stop_filter)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-395-
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-413- lh = khmer._GraphLabels(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:414: asm = khmer.SimpleLabeledAssembler(lh)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-415- paths = asm.assemble(repeat[:K])
##############################################
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-427- graph, contig, L, HDN, R, tip = right_tip_structure
khmer-2.1.2+dfsg/tests/test_cython_assembly.py:428: asm = khmer.JunctionCountAssembler(graph)
khmer-2.1.2+dfsg/tests/test_cython_assembly.py-429- asm.consume(contig)
##############################################
khmer-2.1.2+dfsg/versioneer.py-76-
khmer-2.1.2+dfsg/versioneer.py:77:`_version.py` also contains `$Revision$` markers, and the installation
khmer-2.1.2+dfsg/versioneer.py-78-process marks `_version.py` to have this marker rewritten with a tag name
##############################################
khmer-2.1.2+dfsg/debian/bin/khmer-23-
khmer-2.1.2+dfsg/debian/bin/khmer:24:cmd=`basename "$1" .py`.py
khmer-2.1.2+dfsg/debian/bin/khmer-25-shift