This is an automated email from the git hooks/post-receive script. misterc-guest pushed a change to branch upstream in repository khmer.
from f38372a Imported Upstream version 2.0rc1+dfsg new abe8250 Imported Upstream version 2.0~rc2+dfsg 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: .mailmap | 47 ++ .ycm_extra_conf.py | 105 ---- CITATION | 20 + ChangeLog | 244 ++++++++ MANIFEST.in | 1 + Makefile | 63 +- doc/dev/getting-started.rst | 25 + doc/release-notes/release-1.4.rst | 2 +- doc/user/install.rst | 5 +- doc/user/scripts.rst | 3 + doc/whats-new-2.0.rst | 30 + jenkins-build.sh | 21 +- khmer/__init__.py | 113 +++- khmer/_khmer.cc | 671 ++++++++++++++------- khmer/_version.py | 4 +- khmer/kfile.py | 35 +- khmer/khmer_args.py | 19 +- khmer/thread_utils.py | 2 +- khmer/utils.py | 12 +- lib/Makefile | 220 +++---- lib/counting.cc | 85 ++- lib/counting.hh | 23 +- lib/get_version.py | 1 + lib/hashbits.cc | 30 +- lib/hashbits.hh | 6 + lib/hashtable.cc | 132 ++-- lib/hashtable.hh | 55 +- lib/hllcounter.cc | 35 +- lib/hllcounter.hh | 11 +- lib/ht-diff.cc | 149 ----- lib/khmer_exception.hh | 32 +- lib/kmer_hash.cc | 10 +- lib/labelhash.cc | 33 +- lib/labelhash.hh | 16 +- lib/{khmer.pc.in => oxli.pc.in} | 4 +- lib/perf_metrics.cc | 35 -- lib/perf_metrics.hh | 75 --- lib/read_aligner.cc | 235 ++++++-- lib/read_aligner.hh | 37 +- lib/read_parsers.cc | 25 +- lib/read_parsers.hh | 43 +- lib/subset.cc | 40 +- lib/subset.hh | 10 +- lib/test-HashTables.cc | 150 ----- lib/test-Parser.cc | 145 ----- lib/test-compile.cc | 5 +- lib/trace_logger.cc | 70 --- lib/trace_logger.hh | 76 --- oxli/__init__.py | 6 +- oxli/build_graph.py | 12 +- oxli/functions.py | 129 +++- sandbox/Makefile.read_aligner_training | 26 + sandbox/README.rst | 4 +- sandbox/build-sparse-graph.py | 2 +- sandbox/calc-best-assembly.py | 17 +- sandbox/collect-reads.py | 9 +- sandbox/collect-variants.py | 6 +- sandbox/correct-errors.py | 219 ------- .../trim-low-abund.py => sandbox/correct-reads.py | 246 ++++---- sandbox/count-kmers-single.py | 103 ++++ sandbox/count-kmers.py | 80 +++ sandbox/error-correct-pass2.py | 94 +++ sandbox/estimate_optimal_hash.py | 11 +- sandbox/extract-single-partition.py | 2 +- sandbox/optimal_args_hashbits.py | 2 +- sandbox/readaligner_pairhmm_train.py | 205 +++++++ sandbox/saturate-by-median.py | 4 +- sandbox/sweep-files.py | 8 +- sandbox/sweep-reads.py | 8 +- scripts/abundance-dist-single.py | 34 +- scripts/abundance-dist.py | 32 +- scripts/count-median.py | 36 +- scripts/count-overlap.py | 20 +- scripts/extract-long-sequences.py | 9 +- scripts/extract-paired-reads.py | 4 +- scripts/extract-partitions.py | 3 +- scripts/fastq-to-fasta.py | 7 +- scripts/filter-abund-single.py | 13 +- scripts/filter-abund.py | 18 +- scripts/interleave-reads.py | 31 +- scripts/load-graph.py | 12 +- scripts/load-into-counting.py | 21 +- scripts/make-initial-stoptags.py | 4 +- scripts/normalize-by-median.py | 214 ++++--- scripts/oxli | 16 + scripts/partition-graph.py | 4 +- scripts/readstats.py | 18 +- scripts/sample-reads-randomly.py | 12 +- scripts/split-paired-reads.py | 12 +- scripts/trim-low-abund.py | 30 +- {sandbox => scripts}/unique-kmers.py | 60 +- setup.py | 2 +- tests/khmer_tst_utils.py | 108 ++-- tests/test-data/empty-file.bz2 | Bin 0 -> 14 bytes tests/test-data/empty-file.gz | Bin 0 -> 32 bytes tests/test-data/paired-broken4.fq.1 | 4 + tests/test-data/paired-broken4.fq.2 | 4 + tests/test-data/paired.fq.2 | 1 - tests/test-data/readaligner-default.json | 50 ++ tests/test-data/readaligner-k12.json | 50 ++ tests/test-data/test-fastq-reads.fa | 200 ++++++ tests/test_counting_hash.py | 76 ++- tests/test_counting_single.py | 4 +- tests/test_filter.py | 2 +- tests/test_functions.py | 9 +- tests/test_hashbits.py | 568 ++++++++--------- tests/test_hll.py | 2 +- tests/test_labelhash.py | 12 +- tests/test_lump.py | 4 +- tests/test_normalize_by_median.py | 212 +++++-- tests/test_oxli_functions.py | 40 +- tests/test_read_aligner.py | 502 +++++++++++++-- tests/test_read_parsers.py | 42 +- tests/test_sandbox_scripts.py | 40 +- tests/test_script_arguments.py | 59 +- tests/test_scripts.py | 398 +++++++----- tests/test_streaming_io.py | 451 ++++++++++++++ tests/test_subset_graph.py | 16 +- 118 files changed, 5034 insertions(+), 2835 deletions(-) create mode 100644 .mailmap delete mode 100644 .ycm_extra_conf.py mode change 100644 => 100755 lib/get_version.py delete mode 100644 lib/ht-diff.cc rename lib/{khmer.pc.in => oxli.pc.in} (83%) delete mode 100644 lib/perf_metrics.cc delete mode 100644 lib/perf_metrics.hh delete mode 100644 lib/test-HashTables.cc delete mode 100644 lib/test-Parser.cc delete mode 100644 lib/trace_logger.cc delete mode 100644 lib/trace_logger.hh create mode 100644 sandbox/Makefile.read_aligner_training delete mode 100755 sandbox/correct-errors.py copy scripts/trim-low-abund.py => sandbox/correct-reads.py (52%) create mode 100755 sandbox/count-kmers-single.py create mode 100644 sandbox/count-kmers.py create mode 100755 sandbox/error-correct-pass2.py create mode 100644 sandbox/readaligner_pairhmm_train.py create mode 100755 scripts/oxli rename {sandbox => scripts}/unique-kmers.py (63%) create mode 100644 tests/test-data/empty-file.bz2 create mode 100644 tests/test-data/empty-file.gz create mode 100644 tests/test-data/paired-broken4.fq.1 create mode 100644 tests/test-data/paired-broken4.fq.2 create mode 100644 tests/test-data/readaligner-default.json create mode 100644 tests/test-data/readaligner-k12.json create mode 100644 tests/test-data/test-fastq-reads.fa create mode 100644 tests/test_streaming_io.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