[med-svn] [adapterremoval] branch upstream updated (bdeb331 -> b0e5931)
Andreas Tille
tille at debian.org
Thu Jun 22 07:15:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository adapterremoval.
from bdeb331 New upstream version 2.2.0
new b0e5931 New upstream version 2.2.1
The 1 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 | 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 +-
.../barcodes.txt | 0
.../pe/{defaults => multiple_input}/info.json | 0
.../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 +
.../your_output.sample_1.discarded | 0
.../your_output.sample_1.pair1.truncated | 0
.../your_output.sample_1.pair2.truncated | 0
.../your_output.sample_1.settings | 3 +-
.../your_output.sample_1.singleton.truncated | 0
.../your_output.sample_2.discarded | 0
.../your_output.sample_2.pair1.truncated | 0
.../your_output.sample_2.pair2.truncated | 0
.../your_output.sample_2.settings | 3 +-
.../your_output.sample_2.singleton.truncated | 0
.../one => multiple_input}/your_output.settings | 3 +-
.../your_output.unidentified_1 | 0
.../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 +-
.../multiple_input}/barcodes.txt | 0
.../{pe/defaults => se/multiple_input}/info.json | 0
.../se/multiple_input/input_1a.fastq | 13 ++
.../se/multiple_input/input_1b.fastq | 12 ++
.../se/multiple_input/input_1c.fastq | 8 +
.../your_output.sample_1.discarded | 0
.../your_output.sample_1.settings | 3 +-
.../your_output.sample_1.truncated | 0
.../your_output.sample_2.discarded | 0
.../your_output.sample_2.settings | 3 +-
.../your_output.sample_2.truncated | 0
.../three => multiple_input}/your_output.settings | 3 +-
.../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 +-
.../barcodes.txt | 0
.../pe/multiple_input}/info.json | 0
.../pe/multiple_input/input_1a.fastq | 12 ++
.../pe/multiple_input/input_1b.fastq | 12 ++
.../pe/multiple_input/input_1c.fastq} | 8 +-
.../input_2a.fastq} | 12 +-
.../input_2b.fastq} | 10 +-
.../input_2c.fastq} | 8 +-
.../multiple_input}/your_output.sample_1.discarded | 0
.../your_output.sample_1.pair1.truncated | 0
.../your_output.sample_1.pair2.truncated | 0
.../your_output.sample_1.settings | 3 +-
.../your_output.sample_1.singleton.truncated | 0
.../multiple_input}/your_output.sample_2.discarded | 0
.../your_output.sample_2.pair1.truncated | 0
.../your_output.sample_2.pair2.truncated | 0
.../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 +-
.../multiple_input}/barcodes.txt | 0
.../se/multiple_input}/info.json | 0
.../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 | 0
.../your_output.sample_1.settings | 3 +-
.../your_output.sample_1.truncated | 0
.../multiple_input}/your_output.sample_2.discarded | 0
.../your_output.sample_2.settings | 3 +-
.../your_output.sample_2.truncated | 0
.../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 +
.../input_1.fastq | 0
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 +-
.../incl_adapter/multiple_input}/info.json | 0
.../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 +--
.../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 +-
.../incl_adapter/multiple_input}/info.json | 0
.../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 +
.../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 +
.../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 +
.../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 +
.../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, 2208 insertions(+), 805 deletions(-)
create mode 100644 .travis.yml
copy src/{threads.cc => linereader_joined.cc} (66%)
copy src/{debug.h => linereader_joined.h} (54%)
copy src/main.h => tests/testing.h (65%)
copy validation/demultiplexing/double_indexed/pe/{combined_output => multiple_input}/barcodes.txt (100%)
copy validation/demultiplexing/double_indexed/pe/{defaults => multiple_input}/info.json (100%)
create mode 100644 validation/demultiplexing/double_indexed/pe/multiple_input/input_1a.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/multiple_input/input_1b.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/multiple_input/input_1c.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/multiple_input/input_2a.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/multiple_input/input_2b.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/multiple_input/input_2c.fastq
copy validation/demultiplexing/double_indexed/pe/{defaults => multiple_input}/your_output.sample_1.discarded (100%)
copy validation/demultiplexing/double_indexed/pe/{defaults => multiple_input}/your_output.sample_1.pair1.truncated (100%)
copy validation/demultiplexing/double_indexed/pe/{defaults => multiple_input}/your_output.sample_1.pair2.truncated (100%)
copy validation/demultiplexing/double_indexed/pe/{threads/one => multiple_input}/your_output.sample_1.settings (97%)
copy validation/demultiplexing/double_indexed/pe/{collapse => multiple_input}/your_output.sample_1.singleton.truncated (100%)
copy validation/demultiplexing/double_indexed/pe/{defaults => multiple_input}/your_output.sample_2.discarded (100%)
copy validation/demultiplexing/double_indexed/pe/{defaults => multiple_input}/your_output.sample_2.pair1.truncated (100%)
copy validation/demultiplexing/double_indexed/pe/{defaults => multiple_input}/your_output.sample_2.pair2.truncated (100%)
copy validation/demultiplexing/double_indexed/pe/{threads/one => multiple_input}/your_output.sample_2.settings (97%)
copy validation/demultiplexing/double_indexed/pe/{collapse => multiple_input}/your_output.sample_2.singleton.truncated (100%)
copy validation/demultiplexing/double_indexed/pe/{threads/one => multiple_input}/your_output.settings (93%)
copy validation/demultiplexing/double_indexed/pe/{collapse => multiple_input}/your_output.unidentified_1 (100%)
copy validation/demultiplexing/double_indexed/pe/{collapse => multiple_input}/your_output.unidentified_2 (100%)
copy validation/demultiplexing/double_indexed/{pe/combined_output => se/multiple_input}/barcodes.txt (100%)
copy validation/demultiplexing/double_indexed/{pe/defaults => se/multiple_input}/info.json (100%)
create mode 100644 validation/demultiplexing/double_indexed/se/multiple_input/input_1a.fastq
create mode 100644 validation/demultiplexing/double_indexed/se/multiple_input/input_1b.fastq
create mode 100644 validation/demultiplexing/double_indexed/se/multiple_input/input_1c.fastq
copy validation/demultiplexing/double_indexed/se/{defaults => multiple_input}/your_output.sample_1.discarded (100%)
copy validation/demultiplexing/double_indexed/se/{threads/one => multiple_input}/your_output.sample_1.settings (96%)
copy validation/demultiplexing/double_indexed/se/{defaults => multiple_input}/your_output.sample_1.truncated (100%)
copy validation/demultiplexing/double_indexed/se/{defaults => multiple_input}/your_output.sample_2.discarded (100%)
copy validation/demultiplexing/double_indexed/se/{defaults => multiple_input}/your_output.sample_2.settings (96%)
copy validation/demultiplexing/double_indexed/se/{defaults => multiple_input}/your_output.sample_2.truncated (100%)
copy validation/demultiplexing/double_indexed/se/{threads/three => multiple_input}/your_output.settings (93%)
copy validation/demultiplexing/double_indexed/se/{collapse => multiple_input}/your_output.unidentified (100%)
copy validation/demultiplexing/single_indexed/pe/{combined_output => multiple_input}/barcodes.txt (100%)
copy validation/demultiplexing/{double_indexed/pe/defaults => single_indexed/pe/multiple_input}/info.json (100%)
create mode 100644 validation/demultiplexing/single_indexed/pe/multiple_input/input_1a.fastq
create mode 100644 validation/demultiplexing/single_indexed/pe/multiple_input/input_1b.fastq
copy validation/demultiplexing/{double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq => single_indexed/pe/multiple_input/input_1c.fastq} (50%)
copy validation/demultiplexing/single_indexed/pe/{demux_only/your_output.sample_1.pair2.fastq => multiple_input/input_2a.fastq} (61%)
copy validation/demultiplexing/single_indexed/pe/{combined_output/your_output.sample_1.pair2.truncated => multiple_input/input_2b.fastq} (76%)
copy validation/demultiplexing/single_indexed/pe/{threads/three/your_output.sample_2.pair2.truncated => multiple_input/input_2c.fastq} (66%)
copy validation/demultiplexing/{double_indexed/pe/defaults => single_indexed/pe/multiple_input}/your_output.sample_1.discarded (100%)
copy validation/demultiplexing/single_indexed/pe/{defaults => multiple_input}/your_output.sample_1.pair1.truncated (100%)
copy validation/demultiplexing/single_indexed/pe/{defaults => multiple_input}/your_output.sample_1.pair2.truncated (100%)
copy validation/demultiplexing/single_indexed/pe/{combined_output => multiple_input}/your_output.sample_1.settings (97%)
copy validation/demultiplexing/{double_indexed/pe/collapse => single_indexed/pe/multiple_input}/your_output.sample_1.singleton.truncated (100%)
copy validation/demultiplexing/{double_indexed/pe/defaults => single_indexed/pe/multiple_input}/your_output.sample_2.discarded (100%)
copy validation/demultiplexing/single_indexed/pe/{defaults => multiple_input}/your_output.sample_2.pair1.truncated (100%)
copy validation/demultiplexing/single_indexed/pe/{defaults => multiple_input}/your_output.sample_2.pair2.truncated (100%)
copy validation/demultiplexing/single_indexed/pe/{interleaved/both => multiple_input}/your_output.sample_2.settings (97%)
copy validation/demultiplexing/{double_indexed/pe/collapse => single_indexed/pe/multiple_input}/your_output.sample_2.singleton.truncated (100%)
copy validation/demultiplexing/single_indexed/pe/{interleaved/output => multiple_input}/your_output.settings (93%)
copy validation/demultiplexing/{double_indexed/pe/collapse => single_indexed/pe/multiple_input}/your_output.unidentified_1 (100%)
copy validation/demultiplexing/{double_indexed/pe/collapse => single_indexed/pe/multiple_input}/your_output.unidentified_2 (100%)
copy validation/demultiplexing/single_indexed/{pe/combined_output => se/multiple_input}/barcodes.txt (100%)
copy validation/demultiplexing/{double_indexed/pe/defaults => single_indexed/se/multiple_input}/info.json (100%)
create mode 100644 validation/demultiplexing/single_indexed/se/multiple_input/input_1a.fastq
create mode 100644 validation/demultiplexing/single_indexed/se/multiple_input/input_1b.fastq
create mode 100644 validation/demultiplexing/single_indexed/se/multiple_input/input_1c.fastq
copy validation/demultiplexing/{double_indexed/se/defaults => single_indexed/se/multiple_input}/your_output.sample_1.discarded (100%)
copy validation/demultiplexing/single_indexed/se/{combined_output => multiple_input}/your_output.sample_1.settings (96%)
copy validation/demultiplexing/single_indexed/se/{defaults => multiple_input}/your_output.sample_1.truncated (100%)
copy validation/demultiplexing/{double_indexed/se/defaults => single_indexed/se/multiple_input}/your_output.sample_2.discarded (100%)
copy validation/demultiplexing/single_indexed/se/{threads/one => multiple_input}/your_output.sample_2.settings (96%)
copy validation/demultiplexing/single_indexed/se/{defaults => multiple_input}/your_output.sample_2.truncated (100%)
copy validation/demultiplexing/single_indexed/se/{threads/three => multiple_input}/your_output.settings (93%)
copy validation/demultiplexing/{double_indexed/se/collapse => single_indexed/se/multiple_input}/your_output.unidentified (100%)
create mode 100644 validation/misc/bad_args/fewer_file1/info.json
create mode 100644 validation/misc/bad_args/fewer_file1/input_1a.fastq
create mode 100644 validation/misc/bad_args/fewer_file1/input_1b.fastq
create mode 100644 validation/misc/bad_args/fewer_file1/input_2a.fastq
create mode 100644 validation/misc/bad_args/fewer_file1/input_2b.fastq
create mode 100644 validation/misc/bad_args/fewer_file1/input_2c.fastq
create mode 100644 validation/misc/bad_args/fewer_file2/info.json
create mode 100644 validation/misc/bad_args/fewer_file2/input_1a.fastq
create mode 100644 validation/misc/bad_args/fewer_file2/input_1b.fastq
create mode 100644 validation/misc/bad_args/fewer_file2/input_2a.fastq
create mode 100644 validation/misc/bad_args/negative_window/info.json
copy validation/misc/bad_args/{se_interleaved => negative_window}/input_1.fastq (100%)
copy validation/{demultiplexing/double_indexed/pe/defaults => pe/incl_adapter/multiple_input}/info.json (100%)
create mode 100644 validation/pe/incl_adapter/multiple_input/input_1a.fastq
create mode 100644 validation/pe/incl_adapter/multiple_input/input_1b.fastq
create mode 100644 validation/pe/incl_adapter/multiple_input/input_1c.fastq
create mode 100644 validation/pe/incl_adapter/multiple_input/input_2a.fastq
create mode 100644 validation/pe/incl_adapter/multiple_input/input_2b.fastq
create mode 100644 validation/pe/incl_adapter/multiple_input/input_2c.fastq
copy validation/{misc/bad_args/se_interleaved => pe/incl_adapter/multiple_input}/your_output.discarded (100%)
create mode 100644 validation/pe/incl_adapter/multiple_input/your_output.pair1.truncated
create mode 100644 validation/pe/incl_adapter/multiple_input/your_output.pair2.truncated
copy validation/pe/{excl_adapter/non_overlapping/combined_output/interleaved/keep_both => incl_adapter/multiple_input}/your_output.settings (84%)
copy validation/{misc/bad_args/se_interleaved => pe/incl_adapter/multiple_input}/your_output.singleton.truncated (100%)
copy validation/{demultiplexing/double_indexed/pe/defaults => se/incl_adapter/multiple_input}/info.json (100%)
create mode 100644 validation/se/incl_adapter/multiple_input/input_1a.fastq
create mode 100644 validation/se/incl_adapter/multiple_input/input_1b.fastq
create mode 100644 validation/se/incl_adapter/multiple_input/input_1c.fastq
copy validation/{misc/bad_args/se_interleaved => se/incl_adapter/multiple_input}/your_output.discarded (100%)
copy validation/se/{excl_adapter/combined_output/retained => incl_adapter/multiple_input}/your_output.settings (79%)
create mode 100644 validation/se/incl_adapter/multiple_input/your_output.truncated
create mode 100644 validation/trimwindows/pe/excl_n/info.json
create mode 100644 validation/trimwindows/pe/excl_n/input_1.fastq
create mode 100644 validation/trimwindows/pe/excl_n/input_2.fastq
copy validation/{pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated => trimwindows/pe/excl_n/your_output.discarded} (58%)
copy validation/{misc/bad_args/se_interleaved_input => trimwindows/pe/excl_n}/your_output.pair1.truncated (100%)
copy validation/{misc/bad_args/se_interleaved_input => trimwindows/pe/excl_n}/your_output.pair2.truncated (100%)
copy validation/{pe/incl_adapter/combined_output/interleaved/keep_mate1 => trimwindows/pe/excl_n}/your_output.settings (70%)
create mode 100644 validation/trimwindows/pe/excl_n/your_output.singleton.truncated
create mode 100644 validation/trimwindows/pe/incl_n/info.json
create mode 100644 validation/trimwindows/pe/incl_n/input_1.fastq
create mode 100644 validation/trimwindows/pe/incl_n/input_2.fastq
copy validation/{pe/excl_adapter/overlapping/combined_output/keep_mate1/your_output.pair2.truncated => trimwindows/pe/incl_n/your_output.discarded} (58%)
copy validation/{misc/bad_args/se_interleaved_input => trimwindows/pe/incl_n}/your_output.pair1.truncated (100%)
copy validation/{misc/bad_args/se_interleaved_input => trimwindows/pe/incl_n}/your_output.pair2.truncated (100%)
copy validation/{pe/incl_adapter/combined_output/interleaved/keep_mate1 => trimwindows/pe/incl_n}/your_output.settings (69%)
create mode 100644 validation/trimwindows/pe/incl_n/your_output.singleton.truncated
create mode 100644 validation/trimwindows/se/excl_n/info.json
create mode 100644 validation/trimwindows/se/excl_n/input_1.fastq
copy validation/{misc/bad_args/se_interleaved => trimwindows/se/excl_n}/your_output.discarded (100%)
copy validation/{se/incl_adapter/trimqualities/minq36 => trimwindows/se/excl_n}/your_output.settings (72%)
create mode 100644 validation/trimwindows/se/excl_n/your_output.truncated
create mode 100644 validation/trimwindows/se/incl_n/info.json
create mode 100644 validation/trimwindows/se/incl_n/input_1.fastq
copy validation/{misc/bad_args/se_interleaved => trimwindows/se/incl_n}/your_output.discarded (100%)
copy validation/{se/incl_adapter/trimns/incl_ns => trimwindows/se/incl_n}/your_output.settings (71%)
create mode 100644 validation/trimwindows/se/incl_n/your_output.truncated
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