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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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