[med-svn] [adapterremoval] branch master updated (1decede -> 3383df2)
Andreas Tille
tille at debian.org
Thu Jun 22 07:15:02 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository adapterremoval.
from 1decede Upload to unstable
new b0e5931 New upstream version 2.2.1
new aad41d3 Merge tag 'upstream/2.2.1'
new ad30469 debhelper 10
new 7b33609 verified watch file and set version=4
new 3383df2 Add missing header, upload to unstable
The 5 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 +-
debian/changelog | 9 +
debian/compat | 2 +-
debian/control | 2 +-
debian/patches/add_missing_header.patch | 18 ++
debian/patches/series | 2 +-
debian/patches/spelling.patch | 102 ---------
debian/watch | 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 +
387 files changed, 2239 insertions(+), 911 deletions(-)
create mode 100644 .travis.yml
create mode 100644 debian/patches/add_missing_header.patch
delete mode 100644 debian/patches/spelling.patch
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/{combined_output => 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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