[med-svn] [khmer] branch master updated (e2ed6fe -> 8ea7186)

Michael Crusoe misterc-guest at moszumanska.debian.org
Wed Aug 12 03:11:23 UTC 2015


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misterc-guest pushed a change to branch master
in repository khmer.

      from  e2ed6fe   include missing SphinxDoc depends
      adds  abe8250   Imported Upstream version 2.0~rc2+dfsg
       new  7483ff8   Imported Upstream version 2.0~rc3+dfsg
       new  8ea7186   Merge branch 'upstream'

The 2 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                                         |   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 -
 ...aired-broken2.fq.1 => paired-broken.fq.badleft} |   4 +-
 ...ired-broken3.fq.2 => paired-broken.fq.badright} |   4 +-
 ...ter-abund-Ns.fq => paired-broken.fq.paired_bad} |  10 +-
 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, 4186 insertions(+), 4960 deletions(-)
 create mode 100644 khmer/khmer_logger.py
 create mode 100644 lib/traversal.cc
 create mode 100644 lib/traversal.hh
 delete mode 100755 sandbox/bloom-count-intersection.py
 delete mode 100755 scripts/count-overlap.py
 delete mode 100644 scripts/galaxy/README.txt
 delete mode 100644 scripts/galaxy/abundance-dist-single.xml
 delete mode 100644 scripts/galaxy/abundance-dist.xml
 delete mode 100644 scripts/galaxy/count-median.xml
 delete mode 100644 scripts/galaxy/do-partition.xml
 delete mode 100644 scripts/galaxy/extract-partitions.xml
 delete mode 100644 scripts/galaxy/filter-abund.xml
 delete mode 120000 scripts/galaxy/filter-below-abund.py
 delete mode 100644 scripts/galaxy/filter-below-abund.xml
 delete mode 100644 scripts/galaxy/gedlab.py
 delete mode 100644 scripts/galaxy/macros.xml
 delete mode 100644 scripts/galaxy/normalize-by-median.xml
 delete mode 120000 scripts/galaxy/test-data/random-20-a.fa.part
 delete mode 100644 scripts/galaxy/test-data/test-abund-read-2.ct
 delete mode 100644 scripts/galaxy/test-data/test-abund-read-2.ct.info
 delete mode 120000 scripts/galaxy/test-data/test-abund-read-2.fa
 delete mode 100644 scripts/galaxy/test-data/test-abund-read-2.nobigcount.ct
 delete mode 100644 scripts/galaxy/test-data/test-abund-read-2.nobigcount.ct.info
 delete mode 120000 scripts/galaxy/test-data/test-abund-read-paired.fa
 delete mode 100644 scripts/galaxy/tool_dependencies.xml
 create mode 100644 tests/test-data/multi-output.fa
 delete mode 100644 tests/test-data/overlap.out
 copy tests/test-data/{paired-broken2.fq.1 => paired-broken.fq.badleft} (90%)
 copy tests/test-data/{paired-broken3.fq.2 => paired-broken.fq.badright} (90%)
 copy tests/test-data/{test-filter-abund-Ns.fq => paired-broken.fq.paired_bad} (82%)
 create mode 100644 tests/test-data/test-multi.fa
 rename tests/{test_counting_hash.py => test_countgraph.py} (75%)
 delete mode 100644 tests/test_hashbits.py
 create mode 100644 tests/test_nodegraph.py

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