[med-svn] [adapterremoval] 02/05: Merge tag 'upstream/2.2.1'
Andreas Tille
tille at debian.org
Thu Jun 22 07:15:04 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository adapterremoval.
commit aad41d3aab85a159cdc1796b4298074824846f3f
Merge: 1decede b0e5931
Author: Andreas Tille <tille at debian.org>
Date: Thu Jun 22 08:52:13 2017 +0200
Merge tag 'upstream/2.2.1'
Upstream version 2.2.1
.gitignore | 1 -
.travis.yml | 20 ++
AdapterRemoval.pod | 44 ++--
CHANGES.md | 19 +-
Makefile | 22 +-
README.md | 38 +++-
benchmark/benchmark.sh | 2 +-
benchmark/scripts/evaluate.py | 2 +-
benchmark/scripts/evaluate_dmux.py | 2 +-
benchmark/scripts/evaluate_id.py | 2 +-
benchmark/scripts/extend_profile.py | 2 +-
benchmark/scripts/merge_tables.py | 2 +-
benchmark/scripts/shuffle_fasta.py | 2 +-
benchmark/scripts/tabulate.py | 2 +-
src/adapterset.cc | 2 +-
src/adapterset.h | 6 +-
src/alignment.h | 4 +-
src/argparse.cc | 66 +++++-
src/argparse.h | 52 ++++-
src/debug.h | 11 +-
src/demultiplex.cc | 15 +-
src/demultiplex.h | 9 +-
src/fastq.cc | 113 ++++++++--
src/fastq.h | 39 +++-
src/fastq_enc.h | 4 +-
src/fastq_io.cc | 52 +++--
src/fastq_io.h | 32 ++-
src/linereader.cc | 4 +-
src/linereader.h | 6 +-
src/{threads.cc => linereader_joined.cc} | 68 +++---
src/{debug.h => linereader_joined.h} | 80 +++----
src/main.h | 2 +-
src/main_adapter_id.cc | 14 +-
src/main_adapter_rm.cc | 26 ++-
src/main_demultiplex.cc | 8 +-
src/scheduler.cc | 6 +-
src/scheduler.h | 10 +-
src/strutils.h | 6 +-
src/threads.cc | 14 +-
src/threads.h | 15 +-
src/timer.cc | 3 +-
src/userconfig.cc | 72 ++++---
src/userconfig.h | 7 +-
tests/alignment_test.cc | 1 +
tests/argparse_test.cc | 124 +++++++++++
tests/fastq_test.cc | 229 ++++++++++++++++++---
src/main.h => tests/testing.h | 34 ++-
.../pe/collapse/your_output.sample_1.settings | 3 +-
.../pe/collapse/your_output.sample_2.settings | 3 +-
.../pe/collapse/your_output.settings | 3 +-
.../combined_output/your_output.sample_1.settings | 3 +-
.../combined_output/your_output.sample_2.settings | 3 +-
.../pe/combined_output/your_output.settings | 3 +-
.../pe/defaults/your_output.sample_1.settings | 3 +-
.../pe/defaults/your_output.sample_2.settings | 3 +-
.../pe/defaults/your_output.settings | 3 +-
.../interleaved/both/your_output.sample_1.settings | 3 +-
.../interleaved/both/your_output.sample_2.settings | 3 +-
.../pe/interleaved/both/your_output.settings | 3 +-
.../output/your_output.sample_1.settings | 3 +-
.../output/your_output.sample_2.settings | 3 +-
.../pe/interleaved/output/your_output.settings | 3 +-
.../double_indexed/pe/multiple_input/barcodes.txt | 2 +
.../double_indexed/pe/multiple_input/info.json | 6 +
.../pe/multiple_input/input_1a.fastq | 12 ++
.../pe/multiple_input/input_1b.fastq | 12 ++
.../pe/multiple_input/input_1c.fastq | 8 +
.../pe/multiple_input/input_2a.fastq | 12 ++
.../pe/multiple_input/input_2b.fastq | 12 ++
.../pe/multiple_input/input_2c.fastq | 8 +
.../multiple_input/your_output.sample_1.discarded | 8 +
.../your_output.sample_1.pair1.truncated | 12 ++
.../your_output.sample_1.pair2.truncated | 12 ++
.../your_output.sample_1.settings | 3 +-
.../your_output.sample_1.singleton.truncated | 0
.../multiple_input/your_output.sample_2.discarded | 8 +
.../your_output.sample_2.pair1.truncated | 12 ++
.../your_output.sample_2.pair2.truncated | 12 ++
.../your_output.sample_2.settings | 3 +-
.../your_output.sample_2.singleton.truncated | 0
.../one => multiple_input}/your_output.settings | 3 +-
.../pe/multiple_input/your_output.unidentified_1 | 0
.../pe/multiple_input/your_output.unidentified_2 | 0
.../pe/threads/one/your_output.sample_1.settings | 3 +-
.../pe/threads/one/your_output.sample_2.settings | 3 +-
.../pe/threads/one/your_output.settings | 3 +-
.../pe/threads/three/your_output.sample_1.settings | 3 +-
.../pe/threads/three/your_output.sample_2.settings | 3 +-
.../pe/threads/three/your_output.settings | 3 +-
.../pe/threads/two/your_output.sample_1.settings | 3 +-
.../pe/threads/two/your_output.sample_2.settings | 3 +-
.../pe/threads/two/your_output.settings | 3 +-
.../se/collapse/your_output.sample_1.settings | 3 +-
.../se/collapse/your_output.sample_2.settings | 3 +-
.../se/collapse/your_output.settings | 3 +-
.../combined_output/your_output.sample_1.settings | 3 +-
.../combined_output/your_output.sample_2.settings | 3 +-
.../se/combined_output/your_output.settings | 3 +-
.../se/defaults/your_output.sample_1.settings | 3 +-
.../se/defaults/your_output.sample_2.settings | 3 +-
.../se/defaults/your_output.settings | 3 +-
.../double_indexed/se/multiple_input/barcodes.txt | 2 +
.../double_indexed/se/multiple_input/info.json | 6 +
.../se/multiple_input/input_1a.fastq | 13 ++
.../se/multiple_input/input_1b.fastq | 12 ++
.../se/multiple_input/input_1c.fastq | 8 +
.../multiple_input/your_output.sample_1.discarded | 4 +
.../your_output.sample_1.settings | 3 +-
.../multiple_input/your_output.sample_1.truncated | 12 ++
.../multiple_input/your_output.sample_2.discarded | 4 +
.../your_output.sample_2.settings | 3 +-
.../multiple_input/your_output.sample_2.truncated | 12 ++
.../three => multiple_input}/your_output.settings | 3 +-
.../se/multiple_input/your_output.unidentified | 0
.../se/threads/one/your_output.sample_1.settings | 3 +-
.../se/threads/one/your_output.sample_2.settings | 3 +-
.../se/threads/one/your_output.settings | 3 +-
.../se/threads/three/your_output.sample_1.settings | 3 +-
.../se/threads/three/your_output.sample_2.settings | 3 +-
.../se/threads/three/your_output.settings | 3 +-
.../se/threads/two/your_output.sample_1.settings | 3 +-
.../se/threads/two/your_output.sample_2.settings | 3 +-
.../se/threads/two/your_output.settings | 3 +-
.../pe/collapse/your_output.sample_1.settings | 3 +-
.../pe/collapse/your_output.sample_2.settings | 3 +-
.../pe/collapse/your_output.settings | 3 +-
.../combined_output/your_output.sample_1.settings | 3 +-
.../combined_output/your_output.sample_2.settings | 3 +-
.../pe/combined_output/your_output.settings | 3 +-
.../pe/defaults/your_output.sample_1.settings | 3 +-
.../pe/defaults/your_output.sample_2.settings | 3 +-
.../pe/defaults/your_output.settings | 3 +-
.../interleaved/both/your_output.sample_1.settings | 3 +-
.../interleaved/both/your_output.sample_2.settings | 3 +-
.../pe/interleaved/both/your_output.settings | 3 +-
.../output/your_output.sample_1.settings | 3 +-
.../output/your_output.sample_2.settings | 3 +-
.../pe/interleaved/output/your_output.settings | 3 +-
.../single_indexed/pe/multiple_input/barcodes.txt | 2 +
.../single_indexed/pe/multiple_input/info.json | 6 +
.../pe/multiple_input/input_1a.fastq | 12 ++
.../pe/multiple_input/input_1b.fastq | 12 ++
.../pe/multiple_input/input_1c.fastq | 8 +
.../pe/multiple_input/input_2a.fastq | 12 ++
.../pe/multiple_input/input_2b.fastq | 12 ++
.../pe/multiple_input/input_2c.fastq | 8 +
.../multiple_input/your_output.sample_1.discarded | 8 +
.../your_output.sample_1.pair1.truncated | 12 ++
.../your_output.sample_1.pair2.truncated | 12 ++
.../your_output.sample_1.settings | 3 +-
.../your_output.sample_1.singleton.truncated | 0
.../multiple_input/your_output.sample_2.discarded | 8 +
.../your_output.sample_2.pair1.truncated | 12 ++
.../your_output.sample_2.pair2.truncated | 12 ++
.../your_output.sample_2.settings | 3 +-
.../your_output.sample_2.singleton.truncated | 0
.../output => multiple_input}/your_output.settings | 3 +-
.../pe/multiple_input/your_output.unidentified_1 | 0
.../pe/multiple_input/your_output.unidentified_2 | 0
.../pe/threads/one/your_output.sample_1.settings | 3 +-
.../pe/threads/one/your_output.sample_2.settings | 3 +-
.../pe/threads/one/your_output.settings | 3 +-
.../pe/threads/three/your_output.sample_1.settings | 3 +-
.../pe/threads/three/your_output.sample_2.settings | 3 +-
.../pe/threads/three/your_output.settings | 3 +-
.../pe/threads/two/your_output.sample_1.settings | 3 +-
.../pe/threads/two/your_output.sample_2.settings | 3 +-
.../pe/threads/two/your_output.settings | 3 +-
.../se/collapse/your_output.sample_1.settings | 3 +-
.../se/collapse/your_output.sample_2.settings | 3 +-
.../se/collapse/your_output.settings | 3 +-
.../combined_output/your_output.sample_1.settings | 3 +-
.../combined_output/your_output.sample_2.settings | 3 +-
.../se/combined_output/your_output.settings | 3 +-
.../se/defaults/your_output.sample_1.settings | 3 +-
.../se/defaults/your_output.sample_2.settings | 3 +-
.../se/defaults/your_output.settings | 3 +-
.../single_indexed/se/multiple_input/barcodes.txt | 2 +
.../single_indexed/se/multiple_input/info.json | 6 +
.../se/multiple_input/input_1a.fastq | 8 +
.../se/multiple_input/input_1b.fastq | 12 ++
.../se/multiple_input/input_1c.fastq | 12 ++
.../multiple_input/your_output.sample_1.discarded | 4 +
.../your_output.sample_1.settings | 3 +-
.../multiple_input/your_output.sample_1.truncated | 12 ++
.../multiple_input/your_output.sample_2.discarded | 4 +
.../your_output.sample_2.settings | 3 +-
.../multiple_input/your_output.sample_2.truncated | 12 ++
.../three => multiple_input}/your_output.settings | 3 +-
.../se/multiple_input/your_output.unidentified | 0
.../se/threads/one/your_output.sample_1.settings | 3 +-
.../se/threads/one/your_output.sample_2.settings | 3 +-
.../se/threads/one/your_output.settings | 3 +-
.../se/threads/three/your_output.sample_1.settings | 3 +-
.../se/threads/three/your_output.sample_2.settings | 3 +-
.../se/threads/three/your_output.settings | 3 +-
.../se/threads/two/your_output.sample_1.settings | 3 +-
.../se/threads/two/your_output.sample_2.settings | 3 +-
.../se/threads/two/your_output.settings | 3 +-
validation/misc/bad_args/fewer_file1/info.json | 7 +
.../misc/bad_args/fewer_file1/input_1a.fastq | 16 ++
.../misc/bad_args/fewer_file1/input_1b.fastq | 16 ++
.../misc/bad_args/fewer_file1/input_2a.fastq | 16 ++
.../misc/bad_args/fewer_file1/input_2b.fastq | 16 ++
.../misc/bad_args/fewer_file1/input_2c.fastq | 8 +
validation/misc/bad_args/fewer_file2/info.json | 7 +
.../misc/bad_args/fewer_file2/input_1a.fastq | 16 ++
.../misc/bad_args/fewer_file2/input_1b.fastq | 16 ++
.../misc/bad_args/fewer_file2/input_2a.fastq | 16 ++
validation/misc/bad_args/file2_only/info.json | 2 +-
validation/misc/bad_args/negative_window/info.json | 7 +
.../misc/bad_args/negative_window/input_1.fastq | 8 +
validation/misc/empty/pe/your_output.settings | 3 +-
validation/misc/empty/se/your_output.settings | 3 +-
.../non_overlapping/collapse/your_output.settings | 3 +-
.../combined_output/collapse/your_output.settings | 3 +-
.../interleaved/collapse/your_output.settings | 3 +-
.../interleaved/keep_both/your_output.settings | 3 +-
.../interleaved/keep_mate1/your_output.settings | 7 +-
.../interleaved/keep_mate2/your_output.settings | 7 +-
.../interleaved/keep_neither/your_output.settings | 3 +-
.../combined_output/keep_both/your_output.settings | 3 +-
.../keep_mate1/your_output.settings | 7 +-
.../keep_mate2/your_output.settings | 7 +-
.../keep_neither/your_output.settings | 3 +-
.../crlf_newlines/your_output.settings | 3 +-
.../non_overlapping/defaults/your_output.settings | 3 +-
.../interleaved/both/your_output.settings | 3 +-
.../interleaved/output/your_output.settings | 3 +-
.../maxlength/both/your_output.settings | 3 +-
.../maxlength/mate1/your_output.settings | 7 +-
.../maxlength/mate2/your_output.settings | 7 +-
.../minlength/both/your_output.settings | 3 +-
.../minlength/mate1/your_output.settings | 7 +-
.../minlength/mate2/your_output.settings | 7 +-
.../trimns/excl_ns/your_output.settings | 3 +-
.../trimns/incl_ns/your_output.settings | 3 +-
.../trimqualities/default/your_output.settings | 3 +-
.../trimqualities/minq31/your_output.settings | 3 +-
.../overlapping/collapse/your_output.settings | 3 +-
.../combined_output/collapse/your_output.settings | 3 +-
.../interleaved/collapse/your_output.settings | 3 +-
.../interleaved/keep_both/your_output.settings | 3 +-
.../interleaved/keep_mate1/your_output.settings | 7 +-
.../interleaved/keep_mate2/your_output.settings | 7 +-
.../interleaved/keep_neither/your_output.settings | 3 +-
.../combined_output/keep_both/your_output.settings | 3 +-
.../keep_mate1/your_output.settings | 7 +-
.../keep_mate2/your_output.settings | 7 +-
.../keep_neither/your_output.settings | 3 +-
.../overlapping/crlf_newlines/your_output.settings | 3 +-
.../overlapping/defaults/your_output.settings | 3 +-
.../interleaved/both/your_output.settings | 3 +-
.../interleaved/output/your_output.settings | 3 +-
.../maxlength/both/your_output.settings | 3 +-
.../maxlength/mate1/your_output.settings | 7 +-
.../maxlength/mate2/your_output.settings | 7 +-
.../minlength/both/your_output.settings | 3 +-
.../minlength/mate1/your_output.settings | 7 +-
.../minlength/mate2/your_output.settings | 7 +-
.../trimns/excl_ns/your_output.settings | 3 +-
.../trimns/incl_ns/your_output.settings | 3 +-
.../trimqualities/default/your_output.settings | 3 +-
.../trimqualities/minq31/your_output.settings | 3 +-
.../pe/incl_adapter/collapse/your_output.settings | 3 +-
.../collapse_truncated/your_output.settings | 3 +-
.../combined_output/collapse/your_output.settings | 3 +-
.../collapse_truncated/your_output.settings | 3 +-
.../interleaved/collapse/your_output.settings | 3 +-
.../collapse_truncated/your_output.settings | 3 +-
.../interleaved/keep_both/your_output.settings | 3 +-
.../interleaved/keep_mate1/your_output.settings | 7 +-
.../interleaved/keep_mate2/your_output.settings | 7 +-
.../interleaved/keep_neither/your_output.settings | 3 +-
.../combined_output/keep_both/your_output.settings | 3 +-
.../keep_mate1/your_output.settings | 7 +-
.../keep_mate2/your_output.settings | 7 +-
.../keep_neither/your_output.settings | 3 +-
.../crlf_newlines/your_output.settings | 3 +-
.../pe/incl_adapter/defaults/your_output.settings | 3 +-
.../maxlength/both/your_output.settings | 3 +-
.../maxlength/mate1/your_output.settings | 7 +-
.../maxlength/mate2/your_output.settings | 7 +-
.../minlength/both/your_output.settings | 3 +-
.../minlength/mate1/your_output.settings | 7 +-
.../minlength/mate2/your_output.settings | 7 +-
.../pe/incl_adapter/multiple_input/info.json | 6 +
.../pe/incl_adapter/multiple_input/input_1a.fastq | 16 ++
.../pe/incl_adapter/multiple_input/input_1b.fastq | 16 ++
.../pe/incl_adapter/multiple_input/input_1c.fastq | 8 +
.../pe/incl_adapter/multiple_input/input_2a.fastq | 16 ++
.../pe/incl_adapter/multiple_input/input_2b.fastq | 16 ++
.../pe/incl_adapter/multiple_input/input_2c.fastq | 8 +
.../multiple_input/your_output.discarded | 0
.../multiple_input/your_output.pair1.truncated | 40 ++++
.../multiple_input/your_output.pair2.truncated | 40 ++++
.../multiple_input}/your_output.settings | 25 +--
.../multiple_input/your_output.singleton.truncated | 0
.../incl_adapter/threads/one/your_output.settings | 3 +-
.../threads/three/your_output.settings | 3 +-
.../incl_adapter/threads/two/your_output.settings | 3 +-
.../trimns/excl_ns/your_output.settings | 3 +-
.../trimns/incl_ns/your_output.settings | 3 +-
.../trimqualities/default/your_output.settings | 3 +-
.../trimqualities/minq35/your_output.settings | 3 +-
.../pe/only_adapter/collapse/your_output.settings | 3 +-
.../combined_output/collapse/your_output.settings | 3 +-
.../combined_output/defaults/your_output.settings | 3 +-
.../crlf_newlines/your_output.settings | 3 +-
.../pe/only_adapter/defaults/your_output.settings | 3 +-
.../pe/only_adapter/minlength/your_output.settings | 3 +-
validation/run | 116 ++++++-----
.../se/excl_adapter/collapse/your_output.settings | 3 +-
.../combined_output/collapse/your_output.settings | 3 +-
.../combined_output/discarded/your_output.settings | 3 +-
.../combined_output/retained/your_output.settings | 3 +-
.../crlf_newlines/your_output.settings | 3 +-
.../se/excl_adapter/defaults/your_output.settings | 3 +-
.../se/excl_adapter/maxlength/your_output.settings | 3 +-
.../se/excl_adapter/minlength/your_output.settings | 3 +-
.../trimns/excl_ns/your_output.settings | 3 +-
.../trimns/incl_ns/your_output.settings | 3 +-
.../trimqualities/default/your_output.settings | 3 +-
.../trimqualities/minq31/your_output.settings | 3 +-
.../se/incl_adapter/collapse/your_output.settings | 3 +-
.../collapse_truncated/your_output.settings | 3 +-
.../combined_output/collapse/your_output.settings | 3 +-
.../collapse_truncated/your_output.settings | 3 +-
.../combined_output/discarded/your_output.settings | 3 +-
.../combined_output/retained/your_output.settings | 3 +-
.../crlf_newlines/your_output.settings | 3 +-
.../se/incl_adapter/defaults/your_output.settings | 3 +-
.../se/incl_adapter/maxlength/your_output.settings | 3 +-
.../se/incl_adapter/minlength/your_output.settings | 3 +-
.../se/incl_adapter/multiple_input/info.json | 6 +
.../se/incl_adapter/multiple_input/input_1a.fastq | 16 ++
.../se/incl_adapter/multiple_input/input_1b.fastq | 16 ++
.../se/incl_adapter/multiple_input/input_1c.fastq | 8 +
.../multiple_input/your_output.discarded | 0
.../multiple_input}/your_output.settings | 29 +--
.../multiple_input/your_output.truncated | 40 ++++
.../incl_adapter/threads/one/your_output.settings | 3 +-
.../threads/three/your_output.settings | 3 +-
.../incl_adapter/threads/two/your_output.settings | 3 +-
.../trimns/excl_ns/your_output.settings | 3 +-
.../trimns/incl_ns/your_output.settings | 3 +-
.../trimqualities/default/your_output.settings | 3 +-
.../trimqualities/minq36/your_output.settings | 3 +-
.../se/only_adapter/collapse/your_output.settings | 3 +-
.../combined_output/discarded/your_output.settings | 3 +-
.../combined_output/retained/your_output.settings | 3 +-
.../crlf_newlines/your_output.settings | 3 +-
.../se/only_adapter/defaults/your_output.settings | 3 +-
.../se/only_adapter/minlength/your_output.settings | 3 +-
validation/trimwindows/pe/excl_n/info.json | 6 +
validation/trimwindows/pe/excl_n/input_1.fastq | 4 +
validation/trimwindows/pe/excl_n/input_2.fastq | 4 +
.../trimwindows/pe/excl_n/your_output.discarded | 4 +
.../pe/excl_n/your_output.pair1.truncated | 0
.../pe/excl_n/your_output.pair2.truncated | 0
.../pe/excl_n}/your_output.settings | 41 +---
.../pe/excl_n/your_output.singleton.truncated | 4 +
validation/trimwindows/pe/incl_n/info.json | 6 +
validation/trimwindows/pe/incl_n/input_1.fastq | 4 +
validation/trimwindows/pe/incl_n/input_2.fastq | 4 +
.../trimwindows/pe/incl_n/your_output.discarded | 4 +
.../pe/incl_n/your_output.pair1.truncated | 0
.../pe/incl_n/your_output.pair2.truncated | 0
.../pe/incl_n}/your_output.settings | 42 +---
.../pe/incl_n/your_output.singleton.truncated | 4 +
validation/trimwindows/se/excl_n/info.json | 6 +
validation/trimwindows/se/excl_n/input_1.fastq | 4 +
.../trimwindows/se/excl_n/your_output.discarded | 0
.../se/excl_n}/your_output.settings | 34 +--
.../trimwindows/se/excl_n/your_output.truncated | 4 +
validation/trimwindows/se/incl_n/info.json | 6 +
validation/trimwindows/se/incl_n/input_1.fastq | 4 +
.../trimwindows/se/incl_n/your_output.discarded | 0
.../se/incl_n}/your_output.settings | 36 +---
.../trimwindows/se/incl_n/your_output.truncated | 4 +
380 files changed, 2483 insertions(+), 776 deletions(-)
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