[med-svn] [khmer] 02/02: Merge branch 'upstream'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Aug 12 03:11:24 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository khmer.
commit 8ea7186da036ab103314519dcd03883a0f4b9978
Merge: e2ed6fe 7483ff8
Author: Michael R. Crusoe <crusoe at 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(-)
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