This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch master in repository khmer.
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 been added to this reference. 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/khmer.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit