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commit 8ea7186da036ab103314519dcd03883a0f4b9978 Merge: e2ed6fe 7483ff8 Author: Michael R. Crusoe <cru...@ucdavis.edu> Date: Tue Aug 11 20:10:58 2015 -0700 Merge branch 'upstream' .gitignore | 2 + ChangeLog | 160 +++- Makefile | 14 +- TODO | 10 - doc/dev/coding-guidelines-and-review.rst | 36 +- doc/dev/scripts-and-sandbox.rst | 3 +- doc/user/scripts.rst | 3 - doc/whats-new-2.0.rst | 32 +- khmer/__init__.py | 130 +-- khmer/_khmer.cc | 361 +++----- khmer/_version.py | 4 +- khmer/kfile.py | 53 +- khmer/khmer_args.py | 369 +++++--- khmer/khmer_logger.py | 53 ++ khmer/thread_utils.py | 12 +- khmer/utils.py | 15 +- lib/Makefile | 4 +- lib/counting.cc | 75 +- lib/counting.hh | 46 +- lib/hashbits.cc | 122 +-- lib/hashbits.hh | 98 +-- lib/hashtable.cc | 450 ++-------- lib/hashtable.hh | 171 +--- lib/hllcounter.cc | 19 +- lib/hllcounter.hh | 2 + lib/khmer.hh | 4 + lib/kmer_hash.cc | 67 ++ lib/kmer_hash.hh | 211 +++++ lib/labelhash.cc | 2 +- lib/read_aligner.cc | 76 +- lib/read_parsers.cc | 15 + lib/read_parsers.hh | 2 + lib/subset.cc | 483 +++------- lib/subset.hh | 18 +- lib/traversal.cc | 118 +++ lib/traversal.hh | 56 ++ oxli/__init__.py | 6 +- oxli/build_graph.py | 44 +- oxli/functions.py | 135 --- sandbox/README.rst | 6 +- sandbox/assembly-diff-2.py | 2 +- sandbox/assembly-diff.py | 4 +- sandbox/bloom-count-intersection.py | 61 -- sandbox/bloom-count.py | 2 +- sandbox/build-sparse-graph.py | 2 +- sandbox/calc-error-profile.py | 2 +- sandbox/calc-median-distribution.py | 2 +- sandbox/collect-reads.py | 16 +- sandbox/collect-variants.py | 4 +- sandbox/correct-reads.py | 30 +- sandbox/count-kmers-single.py | 26 +- sandbox/count-kmers.py | 24 +- sandbox/error-correct-pass2.py | 2 +- sandbox/estimate_optimal_hash.py | 3 +- sandbox/fasta-to-abundance-hist.py | 2 +- sandbox/filter-below-abund.py | 2 +- sandbox/filter-median-and-pct.py | 2 +- sandbox/filter-median.py | 2 +- sandbox/find-high-abund-kmers.py | 2 +- sandbox/graph-size.py | 2 +- sandbox/hi-lo-abundance-by-position.py | 2 +- sandbox/multi-rename.py | 7 +- sandbox/normalize-by-median-pct.py | 4 +- sandbox/optimal_args_hashbits.py | 20 +- sandbox/print-stoptags.py | 2 +- sandbox/print-tagset.py | 2 +- sandbox/readaligner_pairhmm_train.py | 2 +- sandbox/saturate-by-median.py | 34 +- sandbox/slice-reads-by-coverage.py | 4 +- sandbox/stoptag-abundance-hist.py | 2 +- sandbox/stoptags-by-position.py | 2 +- sandbox/subset-report.py | 2 +- sandbox/sweep-files.py | 8 +- sandbox/sweep-out-reads-with-contigs.py | 4 +- sandbox/sweep-reads.py | 8 +- sandbox/sweep-reads2.py | 6 +- sandbox/sweep-reads3.py | 6 +- scripts/abundance-dist-single.py | 42 +- scripts/abundance-dist.py | 39 +- scripts/annotate-partitions.py | 6 +- scripts/count-median.py | 20 +- scripts/count-overlap.py | 91 -- scripts/do-partition.py | 43 +- scripts/extract-long-sequences.py | 8 +- scripts/extract-paired-reads.py | 31 +- scripts/extract-partitions.py | 17 +- scripts/fastq-to-fasta.py | 22 +- scripts/filter-abund-single.py | 50 +- scripts/filter-abund.py | 47 +- scripts/filter-stoptags.py | 6 +- scripts/find-knots.py | 34 +- scripts/galaxy/README.txt | 5 - scripts/galaxy/abundance-dist-single.xml | 98 --- scripts/galaxy/abundance-dist.xml | 68 -- scripts/galaxy/count-median.xml | 58 -- scripts/galaxy/do-partition.xml | 107 --- scripts/galaxy/extract-partitions.xml | 77 -- scripts/galaxy/filter-abund.xml | 88 -- scripts/galaxy/filter-below-abund.py | 1 - scripts/galaxy/filter-below-abund.xml | 65 -- scripts/galaxy/gedlab.py | 22 - scripts/galaxy/macros.xml | 160 ---- scripts/galaxy/normalize-by-median.xml | 132 --- scripts/galaxy/test-data/random-20-a.fa.part | 1 - scripts/galaxy/test-data/test-abund-read-2.ct | Bin 20000150 -> 0 bytes scripts/galaxy/test-data/test-abund-read-2.ct.info | 2 - scripts/galaxy/test-data/test-abund-read-2.fa | 1 - .../test-data/test-abund-read-2.nobigcount.ct | Bin 20000130 -> 0 bytes .../test-data/test-abund-read-2.nobigcount.ct.info | 2 - scripts/galaxy/test-data/test-abund-read-paired.fa | 1 - scripts/galaxy/tool_dependencies.xml | 10 - scripts/interleave-reads.py | 23 +- scripts/load-graph.py | 7 +- scripts/load-into-counting.py | 41 +- scripts/make-initial-stoptags.py | 31 +- scripts/merge-partitions.py | 6 +- scripts/normalize-by-median.py | 143 ++- scripts/partition-graph.py | 38 +- scripts/sample-reads-randomly.py | 23 +- scripts/split-paired-reads.py | 112 +-- scripts/trim-low-abund.py | 52 +- scripts/unique-kmers.py | 10 +- setup.py | 15 +- tests/khmer_tst_utils.py | 7 +- tests/test-data/multi-output.fa | 4 + tests/test-data/normC20k20.ct | Bin 40144 -> 3999942 bytes tests/test-data/overlap.out | 7 - tests/test-data/paired-broken.fq.badleft | 8 + tests/test-data/paired-broken.fq.badright | 9 + tests/test-data/paired-broken.fq.paired_bad | 16 + tests/test-data/test-multi.fa | 2 + .../{test_counting_hash.py => test_countgraph.py} | 441 +++++----- tests/test_counting_single.py | 100 +-- tests/test_filter.py | 2 +- tests/test_functions.py | 44 +- tests/test_graph.py | 26 +- tests/test_hashbits.py | 905 ------------------- tests/test_labelhash.py | 58 +- tests/test_lump.py | 20 +- tests/test_nodegraph.py | 977 +++++++++++++++++++++ tests/test_normalize_by_median.py | 79 +- tests/test_oxli_functions.py | 28 +- tests/test_read_aligner.py | 40 +- tests/test_sandbox_scripts.py | 12 + tests/test_script_arguments.py | 39 +- tests/test_scripts.py | 555 ++++++++++-- tests/test_streaming_io.py | 73 +- tests/test_subset_graph.py | 60 +- 148 files changed, 4210 insertions(+), 4951 deletions(-) -- 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