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from a7c2d16 Rename liboxli2=>liboxli1, python3 deps in d/ctrl
new 41a3403 Squash of 'big-rebase' down to one commit
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
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Summary of changes:
.gitignore | 3 +
CITATION | 2 +-
ChangeLog | 354 +-
Doxyfile.in | 2 +-
Makefile | 34 +-
README.rst | 15 +-
debian/control | 48 +-
debian/copyright | 44 +
debian/khmer-common.install | 1 +
.../{liboxli1.postinst => khmer-common.postinst} | 1 +
debian/{liboxli1.postrm => khmer-common.postrm} | 2 +-
debian/khmer.install | 0
debian/liboxli-dev.install | 4 +-
debian/liboxli1.install | 3 +-
debian/patches/get_version | 3 +-
debian/patches/pr-1148-changes | 358 ++
debian/patches/series | 2 +
debian/patches/setup-py-py3 | 8 +
debian/rules | 17 +-
debian/upstream/metadata | 10 +-
doc/conf.py | 2 +-
doc/dev/binary-file-formats.rst | 115 +
doc/dev/development.rst | 6 +-
doc/dev/for-khmer-developers.rst | 4 +-
doc/dev/getting-started.rst | 29 +-
doc/dev/hackathon.rst | 12 +-
doc/dev/index.rst | 1 +
doc/dev/release.rst | 20 +-
doc/dev/scripts-and-sandbox.rst | 2 +-
doc/index.rst | 5 +-
doc/release-notes/release-1.0.1.md | 12 +-
doc/release-notes/release-1.0.1.rst | 14 +-
doc/release-notes/release-1.0.md | 12 +-
doc/release-notes/release-1.0.rst | 16 +-
doc/release-notes/release-1.1.md | 14 +-
doc/release-notes/release-1.1.rst | 14 +-
doc/release-notes/release-1.2.md | 14 +-
doc/release-notes/release-1.2.rst | 14 +-
doc/release-notes/release-1.3.md | 2 +-
doc/release-notes/release-1.3.rst | 2 +-
doc/release-notes/release-1.4.md | 4 +-
doc/release-notes/release-1.4.rst | 4 +-
doc/roadmap.rst | 2 +-
doc/run-corn-50m.sh | 4 +-
doc/user/choosing-table-sizes.rst | 74 +-
doc/user/examples.rst | 4 +-
doc/user/getting-help.rst | 2 +-
doc/user/guide.rst | 2 +-
doc/user/known-issues.rst | 14 +-
doc/user/scripts.rst | 12 +-
doc/whats-new-2.0.rst | 29 +
examples/stamps/do.sh | 4 +-
jenkins-build.sh | 2 +-
khmer/__init__.py | 120 +-
khmer/{_khmermodule.cc => _khmer.cc} | 3792 ++++++++++----------
khmer/_version.py | 11 +-
khmer/kfile.py | 72 +-
khmer/khmer_args.py | 175 +-
khmer/thread_utils.py | 66 +-
khmer/utils.py | 46 +-
lib/.check_openmp.cc | 2 +-
lib/Makefile | 2 +-
lib/counting.cc | 70 +-
lib/counting.hh | 2 +-
lib/get_version.py | 3 +-
lib/graphtest.cc | 4 +-
lib/hashbits.cc | 35 +-
lib/hashbits.hh | 11 +-
lib/hashtable.cc | 119 +-
lib/hashtable.hh | 26 +-
lib/hllcounter.cc | 13 +-
lib/hllcounter.hh | 2 +-
lib/ht-diff.cc | 4 +-
lib/khmer.hh | 12 +-
lib/khmer_exception.hh | 4 +-
lib/kmer_hash.cc | 2 +-
lib/kmer_hash.hh | 2 +-
lib/labelhash.cc | 250 +-
lib/labelhash.hh | 33 +-
lib/magic | 11 +
lib/perf_metrics.cc | 4 +-
lib/perf_metrics.hh | 4 +-
lib/primes.hh | 4 +-
lib/read_aligner.cc | 4 +-
lib/read_aligner.hh | 4 +-
lib/read_parsers.cc | 4 +-
lib/read_parsers.hh | 4 +-
lib/subset.cc | 37 +-
lib/subset.hh | 4 +-
lib/test-Colors.cc | 4 +-
lib/test-HashTables.cc | 4 +-
lib/test-Parser.cc | 4 +-
lib/test-compile.cc | 2 +-
lib/trace_logger.cc | 4 +-
lib/trace_logger.hh | 4 +-
oxli/__init__.py | 55 +
oxli/build_graph.py | 103 +
oxli/functions.py | 103 +
sandbox/README.rst | 230 +-
sandbox/abundance-hist-by-position.py | 16 +-
sandbox/assembly-diff-2.py | 19 +-
sandbox/assembly-diff.py | 16 +-
sandbox/assemstats3.py | 28 +-
sandbox/bloom-count-intersection.py | 25 +-
sandbox/bloom-count.py | 15 +-
sandbox/build-sparse-graph.py | 15 +-
sandbox/calc-best-assembly.py | 25 +-
sandbox/calc-error-profile.py | 40 +-
sandbox/calc-median-distribution.py | 12 +-
sandbox/collect-reads.py | 44 +-
sandbox/collect-variants.py | 49 +-
sandbox/correct-errors.py | 41 +-
sandbox/estimate_optimal_hash.py | 109 +
sandbox/extract-single-partition.py | 9 +-
sandbox/fasta-to-abundance-hist.py | 15 +-
sandbox/filter-below-abund.py | 19 +-
sandbox/filter-median-and-pct.py | 21 +-
sandbox/filter-median.py | 17 +-
sandbox/find-high-abund-kmers.py | 51 +-
sandbox/graph-size.py | 31 +-
sandbox/hi-lo-abundance-by-position.py | 13 +-
sandbox/make-coverage.py | 19 +-
sandbox/multi-rename.py | 9 +-
sandbox/normalize-by-median-pct.py | 82 +-
sandbox/optimal_args_hashbits.py | 97 +
sandbox/print-stoptags.py | 8 +-
sandbox/print-tagset.py | 11 +-
sandbox/renumber-partitions.py | 11 +-
sandbox/saturate-by-median.py | 58 +-
sandbox/shuffle-reverse-rotary.py | 13 +-
sandbox/slice-reads-by-coverage.py | 19 +-
sandbox/split-fasta.py | 11 +-
sandbox/split-sequences-by-length.py | 11 +-
sandbox/stoptag-abundance-hist.py | 11 +-
sandbox/stoptags-by-position.py | 11 +-
sandbox/strip-partition.py | 9 +-
sandbox/subset-report.py | 23 +-
sandbox/sweep-files.py | 51 +-
sandbox/sweep-out-reads-with-contigs.py | 13 +-
sandbox/sweep-reads.py | 121 +-
sandbox/sweep-reads2.py | 43 +-
sandbox/sweep-reads3.py | 43 +-
sandbox/unique-kmers.py | 45 +-
sandbox/write-trimmomatic.py | 11 +-
scripts/abundance-dist-single.py | 67 +-
scripts/abundance-dist.py | 25 +-
scripts/annotate-partitions.py | 17 +-
scripts/count-median.py | 18 +-
scripts/count-overlap.py | 22 +-
scripts/do-partition.py | 94 +-
scripts/extract-long-sequences.py | 7 +-
scripts/extract-paired-reads.py | 113 +-
scripts/extract-partitions.py | 72 +-
scripts/fastq-to-fasta.py | 19 +-
scripts/filter-abund-single.py | 49 +-
scripts/filter-abund.py | 33 +-
scripts/filter-stoptags.py | 13 +-
scripts/find-knots.py | 74 +-
scripts/interleave-reads.py | 41 +-
scripts/load-graph.py | 101 +-
scripts/load-into-counting.py | 50 +-
scripts/make-initial-stoptags.py | 23 +-
scripts/merge-partitions.py | 17 +-
scripts/normalize-by-median.py | 396 +-
scripts/partition-graph.py | 64 +-
scripts/readstats.py | 25 +-
scripts/sample-reads-randomly.py | 42 +-
scripts/split-paired-reads.py | 60 +-
scripts/trim-low-abund.py | 94 +-
setup.cfg | 4 +-
setup.py | 22 +-
tests/__init__.py | 4 +-
tests/khmer_tst_utils.py | 32 +-
tests/test-data/badversion-k32.tagset | Bin 16 -> 20 bytes
tests/test-data/dn-test-all-paired-all-keep.fa | 16 +
tests/test-data/dn-test-none-paired.fa | 8 +
tests/test-data/dn-test-some-paired-all-keep.fa | 12 +
tests/test-data/goodversion-k32.tagset | Bin 34 -> 38 bytes
tests/test-data/normC20k20.ct | Bin 40140 -> 40144 bytes
tests/test-data/paired-slash1.fq | 32 +
tests/test-data/paired-slash1.fq.1 | 16 +
tests/test-data/paired-slash1.fq.2 | 16 +
tests/test-data/paired_one.base.dif.fa | 5 +
...paired-broken3.fq.1 => test-filter-abund-Ns.fq} | 10 +-
tests/test_counting_hash.py | 680 +++-
tests/test_counting_single.py | 90 +-
tests/test_filter.py | 16 +-
tests/test_functions.py | 76 +-
tests/test_graph.py | 46 +-
tests/test_hashbits.py | 327 +-
tests/test_hashbits_obj.py | 563 ---
tests/test_hll.py | 76 +-
tests/test_labelhash.py | 764 ++--
tests/test_lump.py | 31 +-
tests/test_normalize_by_median.py | 627 ++++
tests/test_oxli_functions.py | 60 +
tests/test_read_aligner.py | 18 +-
tests/test_read_parsers.py | 36 +-
tests/test_sandbox_scripts.py | 70 +-
tests/test_script_arguments.py | 218 +-
tests/test_scripts.py | 1384 +++----
tests/test_subset_graph.py | 211 +-
tests/test_threaded_sequence_processor.py | 13 +-
tests/test_version.py | 19 +-
versioneer.py | 1 +
205 files changed, 9123 insertions(+), 6125 deletions(-)
create mode 100644 debian/khmer-common.install
rename debian/{liboxli1.postinst => khmer-common.postinst} (77%)
rename debian/{liboxli1.postrm => khmer-common.postrm} (72%)
mode change 100755 => 100644 debian/khmer.install
create mode 100644 debian/patches/pr-1148-changes
create mode 100644 debian/patches/setup-py-py3
create mode 100644 doc/dev/binary-file-formats.rst
create mode 100644 doc/whats-new-2.0.rst
rename khmer/{_khmermodule.cc => _khmer.cc} (72%)
create mode 100644 lib/magic
create mode 100755 oxli/__init__.py
create mode 100644 oxli/build_graph.py
create mode 100644 oxli/functions.py
create mode 100755 sandbox/estimate_optimal_hash.py
create mode 100644 sandbox/optimal_args_hashbits.py
create mode 100644 tests/test-data/dn-test-all-paired-all-keep.fa
create mode 100644 tests/test-data/dn-test-none-paired.fa
create mode 100644 tests/test-data/dn-test-some-paired-all-keep.fa
create mode 100644 tests/test-data/paired-slash1.fq
create mode 100644 tests/test-data/paired-slash1.fq.1
create mode 100644 tests/test-data/paired-slash1.fq.2
create mode 100644 tests/test-data/paired_one.base.dif.fa
copy tests/test-data/{paired-broken3.fq.1 => test-filter-abund-Ns.fq} (66%)
delete mode 100644 tests/test_hashbits_obj.py
create mode 100644 tests/test_normalize_by_median.py
create mode 100644 tests/test_oxli_functions.py
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