[med-svn] [khmer] branch master updated (41a3403 -> 282f3fd)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Jul 31 16:33:13 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository khmer.
from 41a3403 Squash of 'big-rebase' down to one commit
new 4347c2e Imported Upstream version 2.0~rc2+dfsg
new 282f3fd clean up d/changelog, drop patch, fix tests & install
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:
.mailmap | 47 ++
.ycm_extra_conf.py | 105 ----
CITATION | 20 +
ChangeLog | 244 ++++++++
MANIFEST.in | 1 +
Makefile | 63 +-
debian/changelog | 18 +-
debian/control | 6 +-
debian/liboxli1.install | 2 +-
debian/patches/install-prefix | 11 +
debian/patches/pr-1148-changes | 358 -----------
debian/patches/series | 2 +-
debian/rules | 11 +-
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 +-
125 files changed, 5058 insertions(+), 3219 deletions(-)
create mode 100644 .mailmap
delete mode 100644 .ycm_extra_conf.py
create mode 100644 debian/patches/install-prefix
delete mode 100644 debian/patches/pr-1148-changes
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
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