[med-svn] [adapterremoval] branch master updated (21139d4 -> eda68c5)
Kevin Murray
daube-guest at moszumanska.debian.org
Sat Dec 3 21:38:21 UTC 2016
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a change to branch master
in repository adapterremoval.
from 21139d4 do not yet add benchmarking package
new bdeb331 New upstream version 2.2.0
new f3e92b5 Merge branch 'upstream'
new eda68c5 Bump changelog
The 3 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 | 3 +-
AdapterRemoval.pod | 26 +-
CHANGES.md | 33 +-
Makefile | 83 ++--
README.md | 58 ++-
debian/changelog | 7 +-
examples/Makefile | 47 ++
src/adapterset.cc | 9 +-
src/alignment.cc | 12 +-
src/alignment.h | 10 +-
src/argparse.cc | 31 +-
src/debug.cc | 10 +-
src/debug.h | 6 +-
src/demultiplex.cc | 180 +++-----
src/demultiplex.h | 9 +-
src/fastq.cc | 18 +-
src/fastq.h | 12 +-
src/fastq_enc.cc | 17 +-
src/fastq_enc.h | 6 +-
src/fastq_io.cc | 108 ++---
src/fastq_io.h | 30 +-
src/linereader.cc | 9 +-
src/main.cc | 35 +-
src/main.h | 2 +-
src/main_adapter_id.cc | 46 +-
src/main_adapter_rm.cc | 484 ++++++++++----------
src/main_demultiplex.cc | 402 +++++++++++++++++
src/scheduler.cc | 465 +++++++------------
src/scheduler.h | 140 +++---
src/strutils.cc | 7 +
src/strutils.h | 2 +-
src/threads.cc | 279 +-----------
src/threads.h | 124 +----
src/trimmed_reads.cc | 164 +++++++
src/trimmed_reads.h | 172 +++++++
src/userconfig.cc | 131 ++++--
src/userconfig.h | 62 +--
tests/alignment_test.cc | 49 +-
tests/argparse_test.cc | 2 +-
tests/fastq_test.cc | 60 +++
validation/README | 60 +++
.../double_indexed/pe/collapse/barcodes.txt | 2 +
.../double_indexed/pe/collapse/info.json | 6 +
.../double_indexed/pe/collapse/input_1.fastq | 32 ++
.../double_indexed/pe/collapse/input_2.fastq | 32 ++
.../pe/collapse/your_output.sample_1.collapsed | 8 +
.../your_output.sample_1.collapsed.truncated | 0
.../pe/collapse/your_output.sample_1.discarded | 4 +
.../collapse/your_output.sample_1.pair1.truncated | 4 +
.../collapse/your_output.sample_1.pair2.truncated | 4 +
.../pe/collapse/your_output.sample_1.settings | 207 +++++++++
.../your_output.sample_1.singleton.truncated | 0
.../pe/collapse/your_output.sample_2.collapsed | 8 +
.../your_output.sample_2.collapsed.truncated | 0
.../pe/collapse/your_output.sample_2.discarded | 4 +
.../collapse/your_output.sample_2.pair1.truncated | 4 +
.../collapse/your_output.sample_2.pair2.truncated | 4 +
.../pe/collapse/your_output.sample_2.settings | 207 +++++++++
.../your_output.sample_2.singleton.truncated | 0
.../pe/collapse/your_output.settings | 45 ++
.../pe/collapse/your_output.unidentified_1 | 0
.../pe/collapse/your_output.unidentified_2 | 0
.../double_indexed/pe/combined_output/barcodes.txt | 2 +
.../double_indexed/pe/combined_output/info.json | 6 +
.../pe/combined_output/input_1.fastq | 32 ++
.../pe/combined_output/input_2.fastq | 32 ++
.../your_output.sample_1.pair1.truncated | 16 +
.../your_output.sample_1.pair2.truncated | 16 +
.../combined_output/your_output.sample_1.settings | 147 ++++++
.../your_output.sample_2.pair1.truncated | 16 +
.../your_output.sample_2.pair2.truncated | 16 +
.../combined_output/your_output.sample_2.settings | 147 ++++++
.../pe/combined_output/your_output.settings | 45 ++
.../pe/combined_output/your_output.unidentified_1 | 0
.../pe/combined_output/your_output.unidentified_2 | 0
.../double_indexed/pe/defaults/barcodes.txt | 2 +
.../double_indexed/pe/defaults/info.json | 6 +
.../double_indexed/pe/defaults/input_1.fastq | 32 ++
.../double_indexed/pe/defaults/input_2.fastq | 32 ++
.../pe/defaults/your_output.sample_1.discarded | 8 +
.../defaults/your_output.sample_1.pair1.truncated | 12 +
.../defaults/your_output.sample_1.pair2.truncated | 12 +
.../pe/defaults/your_output.sample_1.settings | 147 ++++++
.../your_output.sample_1.singleton.truncated | 0
.../pe/defaults/your_output.sample_2.discarded | 8 +
.../defaults/your_output.sample_2.pair1.truncated | 12 +
.../defaults/your_output.sample_2.pair2.truncated | 12 +
.../pe/defaults/your_output.sample_2.settings | 147 ++++++
.../your_output.sample_2.singleton.truncated | 0
.../pe/defaults/your_output.settings | 45 ++
.../pe/defaults/your_output.unidentified_1 | 0
.../pe/defaults/your_output.unidentified_2 | 0
.../pe/demux_only/interleaved/barcodes.txt | 2 +
.../pe/demux_only/interleaved/info.json | 6 +
.../pe/demux_only/interleaved/input_1.fastq | 32 ++
.../pe/demux_only/interleaved/input_2.fastq | 32 ++
.../interleaved/your_output.sample_1.paired.fastq | 32 ++
.../interleaved/your_output.sample_1.settings | 19 +
.../interleaved/your_output.sample_2.paired.fastq | 32 ++
.../interleaved/your_output.sample_2.settings | 19 +
.../pe/demux_only/interleaved/your_output.settings | 28 ++
.../your_output.unidentified.paired.fastq | 0
.../pe/demux_only/regular/barcodes.txt | 2 +
.../double_indexed/pe/demux_only/regular/info.json | 6 +
.../pe/demux_only/regular/input_1.fastq | 32 ++
.../pe/demux_only/regular/input_2.fastq | 32 ++
.../regular/your_output.sample_1.pair1.fastq | 16 +
.../regular/your_output.sample_1.pair2.fastq | 16 +
.../regular/your_output.sample_1.settings | 19 +
.../regular/your_output.sample_2.pair1.fastq | 16 +
.../regular/your_output.sample_2.pair2.fastq | 16 +
.../regular/your_output.sample_2.settings | 19 +
.../pe/demux_only/regular/your_output.settings | 28 ++
.../regular/your_output.unidentified_1.fastq | 0
.../regular/your_output.unidentified_2.fastq | 0
.../pe/demux_only/unidentified/barcodes.txt | 2 +
.../pe/demux_only/unidentified/info.json | 6 +
.../pe/demux_only/unidentified/input_1.fastq | 32 ++
.../pe/demux_only/unidentified/input_2.fastq | 32 ++
.../unidentified/your_output.sample_1.pair1.fastq | 12 +
.../unidentified/your_output.sample_1.pair2.fastq | 12 +
.../unidentified/your_output.sample_1.settings | 19 +
.../unidentified/your_output.sample_2.pair1.fastq | 12 +
.../unidentified/your_output.sample_2.pair2.fastq | 12 +
.../unidentified/your_output.sample_2.settings | 19 +
.../demux_only/unidentified/your_output.settings | 28 ++
.../unidentified/your_output.unidentified_1.fastq | 8 +
.../unidentified/your_output.unidentified_2.fastq | 8 +
.../pe/interleaved/both/barcodes.txt | 2 +
.../double_indexed/pe/interleaved/both/info.json | 6 +
.../pe/interleaved/both/input_1.fastq | 64 +++
.../both/your_output.sample_1.discarded | 8 +
.../both/your_output.sample_1.paired.truncated | 24 +
.../interleaved/both/your_output.sample_1.settings | 147 ++++++
.../both/your_output.sample_1.singleton.truncated | 0
.../both/your_output.sample_2.discarded | 8 +
.../both/your_output.sample_2.paired.truncated | 24 +
.../interleaved/both/your_output.sample_2.settings | 147 ++++++
.../both/your_output.sample_2.singleton.truncated | 0
.../pe/interleaved/both/your_output.settings | 45 ++
.../both/your_output.unidentified.paired | 0
.../pe/interleaved/output/barcodes.txt | 2 +
.../double_indexed/pe/interleaved/output/info.json | 6 +
.../pe/interleaved/output/input_1.fastq | 32 ++
.../pe/interleaved/output/input_2.fastq | 32 ++
.../output/your_output.sample_1.discarded | 8 +
.../output/your_output.sample_1.paired.truncated | 24 +
.../output/your_output.sample_1.settings | 147 ++++++
.../your_output.sample_1.singleton.truncated | 0
.../output/your_output.sample_2.discarded | 8 +
.../output/your_output.sample_2.paired.truncated | 24 +
.../output/your_output.sample_2.settings | 147 ++++++
.../your_output.sample_2.singleton.truncated | 0
.../pe/interleaved/output/your_output.settings | 45 ++
.../output/your_output.unidentified.paired | 0
.../double_indexed/pe/threads/one/barcodes.txt | 2 +
.../double_indexed/pe/threads/one/info.json | 6 +
.../double_indexed/pe/threads/one/input_1.fastq | 32 ++
.../double_indexed/pe/threads/one/input_2.fastq | 32 ++
.../pe/threads/one/your_output.sample_1.discarded | 8 +
.../one/your_output.sample_1.pair1.truncated | 12 +
.../one/your_output.sample_1.pair2.truncated | 12 +
.../pe/threads/one/your_output.sample_1.settings | 147 ++++++
.../one/your_output.sample_1.singleton.truncated | 0
.../pe/threads/one/your_output.sample_2.discarded | 8 +
.../one/your_output.sample_2.pair1.truncated | 12 +
.../one/your_output.sample_2.pair2.truncated | 12 +
.../pe/threads/one/your_output.sample_2.settings | 147 ++++++
.../one/your_output.sample_2.singleton.truncated | 0
.../pe/threads/one/your_output.settings | 45 ++
.../pe/threads/one/your_output.unidentified_1 | 0
.../pe/threads/one/your_output.unidentified_2 | 0
.../double_indexed/pe/threads/three/barcodes.txt | 2 +
.../double_indexed/pe/threads/three/info.json | 6 +
.../double_indexed/pe/threads/three/input_1.fastq | 32 ++
.../double_indexed/pe/threads/three/input_2.fastq | 32 ++
.../threads/three/your_output.sample_1.discarded | 8 +
.../three/your_output.sample_1.pair1.truncated | 12 +
.../three/your_output.sample_1.pair2.truncated | 12 +
.../pe/threads/three/your_output.sample_1.settings | 147 ++++++
.../three/your_output.sample_1.singleton.truncated | 0
.../threads/three/your_output.sample_2.discarded | 8 +
.../three/your_output.sample_2.pair1.truncated | 12 +
.../three/your_output.sample_2.pair2.truncated | 12 +
.../pe/threads/three/your_output.sample_2.settings | 147 ++++++
.../three/your_output.sample_2.singleton.truncated | 0
.../pe/threads/three/your_output.settings | 45 ++
.../pe/threads/three/your_output.unidentified_1 | 0
.../pe/threads/three/your_output.unidentified_2 | 0
.../double_indexed/pe/threads/two/barcodes.txt | 2 +
.../double_indexed/pe/threads/two/info.json | 6 +
.../double_indexed/pe/threads/two/input_1.fastq | 32 ++
.../double_indexed/pe/threads/two/input_2.fastq | 32 ++
.../pe/threads/two/your_output.sample_1.discarded | 8 +
.../two/your_output.sample_1.pair1.truncated | 12 +
.../two/your_output.sample_1.pair2.truncated | 12 +
.../pe/threads/two/your_output.sample_1.settings | 147 ++++++
.../two/your_output.sample_1.singleton.truncated | 0
.../pe/threads/two/your_output.sample_2.discarded | 8 +
.../two/your_output.sample_2.pair1.truncated | 12 +
.../two/your_output.sample_2.pair2.truncated | 12 +
.../pe/threads/two/your_output.sample_2.settings | 147 ++++++
.../two/your_output.sample_2.singleton.truncated | 0
.../pe/threads/two/your_output.settings | 45 ++
.../pe/threads/two/your_output.unidentified_1 | 0
.../pe/threads/two/your_output.unidentified_2 | 0
.../double_indexed/se/collapse/barcodes.txt | 2 +
.../double_indexed/se/collapse/info.json | 6 +
.../double_indexed/se/collapse/input_1.fastq | 32 ++
.../se/collapse/your_output.sample_1.collapsed | 4 +
.../your_output.sample_1.collapsed.truncated | 0
.../se/collapse/your_output.sample_1.discarded | 4 +
.../se/collapse/your_output.sample_1.settings | 146 ++++++
.../se/collapse/your_output.sample_1.truncated | 8 +
.../se/collapse/your_output.sample_2.collapsed | 4 +
.../your_output.sample_2.collapsed.truncated | 0
.../se/collapse/your_output.sample_2.discarded | 4 +
.../se/collapse/your_output.sample_2.settings | 146 ++++++
.../se/collapse/your_output.sample_2.truncated | 8 +
.../se/collapse/your_output.settings | 44 ++
.../se/collapse/your_output.unidentified | 0
.../double_indexed/se/combined_output/barcodes.txt | 2 +
.../double_indexed/se/combined_output/info.json | 6 +
.../se/combined_output/input_1.fastq | 32 ++
.../combined_output/your_output.sample_1.settings | 144 ++++++
.../combined_output/your_output.sample_1.truncated | 16 +
.../combined_output/your_output.sample_2.settings | 144 ++++++
.../combined_output/your_output.sample_2.truncated | 16 +
.../se/combined_output/your_output.settings | 44 ++
.../se/combined_output/your_output.unidentified | 0
.../double_indexed/se/defaults/barcodes.txt | 2 +
.../double_indexed/se/defaults/info.json | 6 +
.../double_indexed/se/defaults/input_1.fastq | 32 ++
.../se/defaults/your_output.sample_1.discarded | 4 +
.../se/defaults/your_output.sample_1.settings | 144 ++++++
.../se/defaults/your_output.sample_1.truncated | 12 +
.../se/defaults/your_output.sample_2.discarded | 4 +
.../se/defaults/your_output.sample_2.settings | 144 ++++++
.../se/defaults/your_output.sample_2.truncated | 12 +
.../se/defaults/your_output.settings | 44 ++
.../se/defaults/your_output.unidentified | 0
.../se/demux_only/regular/barcodes.txt | 2 +
.../double_indexed/se/demux_only/regular/info.json | 6 +
.../se/demux_only/regular/input_1.fastq | 32 ++
.../demux_only/regular/your_output.sample_1.fastq | 16 +
.../regular/your_output.sample_1.settings | 17 +
.../demux_only/regular/your_output.sample_2.fastq | 16 +
.../regular/your_output.sample_2.settings | 17 +
.../se/demux_only/regular/your_output.settings | 26 ++
.../regular/your_output.unidentified.fastq | 0
.../se/demux_only/unidentified/barcodes.txt | 2 +
.../se/demux_only/unidentified/info.json | 6 +
.../se/demux_only/unidentified/input_1.fastq | 32 ++
.../unidentified/your_output.sample_1.fastq | 12 +
.../unidentified/your_output.sample_1.settings | 17 +
.../unidentified/your_output.sample_2.fastq | 16 +
.../unidentified/your_output.sample_2.settings | 17 +
.../demux_only/unidentified/your_output.settings | 26 ++
.../unidentified/your_output.unidentified.fastq | 4 +
.../double_indexed/se/threads/one/barcodes.txt | 2 +
.../double_indexed/se/threads/one/info.json | 6 +
.../double_indexed/se/threads/one/input_1.fastq | 32 ++
.../se/threads/one/your_output.sample_1.discarded | 4 +
.../se/threads/one/your_output.sample_1.settings | 144 ++++++
.../se/threads/one/your_output.sample_1.truncated | 12 +
.../se/threads/one/your_output.sample_2.discarded | 4 +
.../se/threads/one/your_output.sample_2.settings | 144 ++++++
.../se/threads/one/your_output.sample_2.truncated | 12 +
.../se/threads/one/your_output.settings | 44 ++
.../se/threads/one/your_output.unidentified | 0
.../double_indexed/se/threads/three/barcodes.txt | 2 +
.../double_indexed/se/threads/three/info.json | 6 +
.../double_indexed/se/threads/three/input_1.fastq | 32 ++
.../threads/three/your_output.sample_1.discarded | 4 +
.../se/threads/three/your_output.sample_1.settings | 144 ++++++
.../threads/three/your_output.sample_1.truncated | 12 +
.../threads/three/your_output.sample_2.discarded | 4 +
.../se/threads/three/your_output.sample_2.settings | 144 ++++++
.../threads/three/your_output.sample_2.truncated | 12 +
.../se/threads/three/your_output.settings | 44 ++
.../se/threads/three/your_output.unidentified | 0
.../double_indexed/se/threads/two/barcodes.txt | 2 +
.../double_indexed/se/threads/two/info.json | 6 +
.../double_indexed/se/threads/two/input_1.fastq | 32 ++
.../se/threads/two/your_output.sample_1.discarded | 4 +
.../se/threads/two/your_output.sample_1.settings | 144 ++++++
.../se/threads/two/your_output.sample_1.truncated | 12 +
.../se/threads/two/your_output.sample_2.discarded | 4 +
.../se/threads/two/your_output.sample_2.settings | 144 ++++++
.../se/threads/two/your_output.sample_2.truncated | 12 +
.../se/threads/two/your_output.settings | 44 ++
.../se/threads/two/your_output.unidentified | 0
.../single_indexed/pe/collapse/barcodes.txt | 2 +
.../single_indexed/pe/collapse/info.json | 6 +
.../single_indexed/pe/collapse/input_1.fastq | 32 ++
.../single_indexed/pe/collapse/input_2.fastq | 32 ++
.../pe/collapse/your_output.sample_1.collapsed | 8 +
.../your_output.sample_1.collapsed.truncated | 0
.../pe/collapse/your_output.sample_1.discarded | 4 +
.../collapse/your_output.sample_1.pair1.truncated | 4 +
.../collapse/your_output.sample_1.pair2.truncated | 4 +
.../pe/collapse/your_output.sample_1.settings | 207 +++++++++
.../your_output.sample_1.singleton.truncated | 0
.../pe/collapse/your_output.sample_2.collapsed | 8 +
.../your_output.sample_2.collapsed.truncated | 0
.../pe/collapse/your_output.sample_2.discarded | 4 +
.../collapse/your_output.sample_2.pair1.truncated | 4 +
.../collapse/your_output.sample_2.pair2.truncated | 4 +
.../pe/collapse/your_output.sample_2.settings | 207 +++++++++
.../your_output.sample_2.singleton.truncated | 0
.../pe/collapse/your_output.settings | 45 ++
.../pe/collapse/your_output.unidentified_1 | 0
.../pe/collapse/your_output.unidentified_2 | 0
.../single_indexed/pe/combined_output/barcodes.txt | 2 +
.../single_indexed/pe/combined_output/info.json | 6 +
.../pe/combined_output/input_1.fastq | 32 ++
.../pe/combined_output/input_2.fastq | 32 ++
.../your_output.sample_1.pair1.truncated | 16 +
.../your_output.sample_1.pair2.truncated | 16 +
.../combined_output/your_output.sample_1.settings | 155 +++++++
.../your_output.sample_2.pair1.truncated | 16 +
.../your_output.sample_2.pair2.truncated | 16 +
.../combined_output/your_output.sample_2.settings | 155 +++++++
.../pe/combined_output/your_output.settings | 45 ++
.../pe/combined_output/your_output.unidentified_1 | 0
.../pe/combined_output/your_output.unidentified_2 | 0
.../single_indexed/pe/defaults/barcodes.txt | 2 +
.../single_indexed/pe/defaults/info.json | 6 +
.../single_indexed/pe/defaults/input_1.fastq | 32 ++
.../single_indexed/pe/defaults/input_2.fastq | 32 ++
.../pe/defaults/your_output.sample_1.discarded | 8 +
.../defaults/your_output.sample_1.pair1.truncated | 12 +
.../defaults/your_output.sample_1.pair2.truncated | 12 +
.../pe/defaults/your_output.sample_1.settings | 155 +++++++
.../your_output.sample_1.singleton.truncated | 0
.../pe/defaults/your_output.sample_2.discarded | 8 +
.../defaults/your_output.sample_2.pair1.truncated | 12 +
.../defaults/your_output.sample_2.pair2.truncated | 12 +
.../pe/defaults/your_output.sample_2.settings | 155 +++++++
.../your_output.sample_2.singleton.truncated | 0
.../pe/defaults/your_output.settings | 45 ++
.../pe/defaults/your_output.unidentified_1 | 0
.../pe/defaults/your_output.unidentified_2 | 0
.../single_indexed/pe/demux_only/barcodes.txt | 2 +
.../single_indexed/pe/demux_only/info.json | 6 +
.../single_indexed/pe/demux_only/input_1.fastq | 32 ++
.../single_indexed/pe/demux_only/input_2.fastq | 32 ++
.../pe/demux_only/your_output.sample_1.pair1.fastq | 16 +
.../pe/demux_only/your_output.sample_1.pair2.fastq | 16 +
.../pe/demux_only/your_output.sample_1.settings | 19 +
.../pe/demux_only/your_output.sample_2.pair1.fastq | 16 +
.../pe/demux_only/your_output.sample_2.pair2.fastq | 16 +
.../pe/demux_only/your_output.sample_2.settings | 19 +
.../pe/demux_only/your_output.settings | 28 ++
.../pe/demux_only/your_output.unidentified_1.fastq | 0
.../pe/demux_only/your_output.unidentified_2.fastq | 0
.../pe/interleaved/both/barcodes.txt | 2 +
.../single_indexed/pe/interleaved/both/info.json | 6 +
.../pe/interleaved/both/input_1.fastq | 64 +++
.../both/your_output.sample_1.discarded | 8 +
.../both/your_output.sample_1.paired.truncated | 24 +
.../interleaved/both/your_output.sample_1.settings | 155 +++++++
.../both/your_output.sample_1.singleton.truncated | 0
.../both/your_output.sample_2.discarded | 8 +
.../both/your_output.sample_2.paired.truncated | 24 +
.../interleaved/both/your_output.sample_2.settings | 155 +++++++
.../both/your_output.sample_2.singleton.truncated | 0
.../pe/interleaved/both/your_output.settings | 45 ++
.../both/your_output.unidentified.paired | 0
.../pe/interleaved/output/barcodes.txt | 2 +
.../single_indexed/pe/interleaved/output/info.json | 6 +
.../pe/interleaved/output/input_1.fastq | 32 ++
.../pe/interleaved/output/input_2.fastq | 32 ++
.../output/your_output.sample_1.discarded | 8 +
.../output/your_output.sample_1.paired.truncated | 24 +
.../output/your_output.sample_1.settings | 155 +++++++
.../your_output.sample_1.singleton.truncated | 0
.../output/your_output.sample_2.discarded | 8 +
.../output/your_output.sample_2.paired.truncated | 24 +
.../output/your_output.sample_2.settings | 155 +++++++
.../your_output.sample_2.singleton.truncated | 0
.../pe/interleaved/output/your_output.settings | 45 ++
.../output/your_output.unidentified.paired | 0
.../single_indexed/pe/threads/one/barcodes.txt | 2 +
.../single_indexed/pe/threads/one/info.json | 6 +
.../single_indexed/pe/threads/one/input_1.fastq | 32 ++
.../single_indexed/pe/threads/one/input_2.fastq | 32 ++
.../pe/threads/one/your_output.sample_1.discarded | 8 +
.../one/your_output.sample_1.pair1.truncated | 12 +
.../one/your_output.sample_1.pair2.truncated | 12 +
.../pe/threads/one/your_output.sample_1.settings | 155 +++++++
.../one/your_output.sample_1.singleton.truncated | 0
.../pe/threads/one/your_output.sample_2.discarded | 8 +
.../one/your_output.sample_2.pair1.truncated | 12 +
.../one/your_output.sample_2.pair2.truncated | 12 +
.../pe/threads/one/your_output.sample_2.settings | 155 +++++++
.../one/your_output.sample_2.singleton.truncated | 0
.../pe/threads/one/your_output.settings | 45 ++
.../pe/threads/one/your_output.unidentified_1 | 0
.../pe/threads/one/your_output.unidentified_2 | 0
.../single_indexed/pe/threads/three/barcodes.txt | 2 +
.../single_indexed/pe/threads/three/info.json | 6 +
.../single_indexed/pe/threads/three/input_1.fastq | 32 ++
.../single_indexed/pe/threads/three/input_2.fastq | 32 ++
.../threads/three/your_output.sample_1.discarded | 8 +
.../three/your_output.sample_1.pair1.truncated | 12 +
.../three/your_output.sample_1.pair2.truncated | 12 +
.../pe/threads/three/your_output.sample_1.settings | 155 +++++++
.../three/your_output.sample_1.singleton.truncated | 0
.../threads/three/your_output.sample_2.discarded | 8 +
.../three/your_output.sample_2.pair1.truncated | 12 +
.../three/your_output.sample_2.pair2.truncated | 12 +
.../pe/threads/three/your_output.sample_2.settings | 155 +++++++
.../three/your_output.sample_2.singleton.truncated | 0
.../pe/threads/three/your_output.settings | 45 ++
.../pe/threads/three/your_output.unidentified_1 | 0
.../pe/threads/three/your_output.unidentified_2 | 0
.../single_indexed/pe/threads/two/barcodes.txt | 2 +
.../single_indexed/pe/threads/two/info.json | 6 +
.../single_indexed/pe/threads/two/input_1.fastq | 32 ++
.../single_indexed/pe/threads/two/input_2.fastq | 32 ++
.../pe/threads/two/your_output.sample_1.discarded | 8 +
.../two/your_output.sample_1.pair1.truncated | 12 +
.../two/your_output.sample_1.pair2.truncated | 12 +
.../pe/threads/two/your_output.sample_1.settings | 155 +++++++
.../two/your_output.sample_1.singleton.truncated | 0
.../pe/threads/two/your_output.sample_2.discarded | 8 +
.../two/your_output.sample_2.pair1.truncated | 12 +
.../two/your_output.sample_2.pair2.truncated | 12 +
.../pe/threads/two/your_output.sample_2.settings | 155 +++++++
.../two/your_output.sample_2.singleton.truncated | 0
.../pe/threads/two/your_output.settings | 45 ++
.../pe/threads/two/your_output.unidentified_1 | 0
.../pe/threads/two/your_output.unidentified_2 | 0
.../single_indexed/se/collapse/barcodes.txt | 2 +
.../single_indexed/se/collapse/info.json | 6 +
.../single_indexed/se/collapse/input_1.fastq | 32 ++
.../se/collapse/your_output.sample_1.collapsed | 4 +
.../your_output.sample_1.collapsed.truncated | 0
.../se/collapse/your_output.sample_1.discarded | 4 +
.../se/collapse/your_output.sample_1.settings | 146 ++++++
.../se/collapse/your_output.sample_1.truncated | 8 +
.../se/collapse/your_output.sample_2.collapsed | 4 +
.../your_output.sample_2.collapsed.truncated | 0
.../se/collapse/your_output.sample_2.discarded | 4 +
.../se/collapse/your_output.sample_2.settings | 146 ++++++
.../se/collapse/your_output.sample_2.truncated | 8 +
.../se/collapse/your_output.settings | 44 ++
.../se/collapse/your_output.unidentified | 0
.../single_indexed/se/combined_output/barcodes.txt | 2 +
.../single_indexed/se/combined_output/info.json | 6 +
.../se/combined_output/input_1.fastq | 32 ++
.../combined_output/your_output.sample_1.settings | 144 ++++++
.../combined_output/your_output.sample_1.truncated | 16 +
.../combined_output/your_output.sample_2.settings | 144 ++++++
.../combined_output/your_output.sample_2.truncated | 16 +
.../se/combined_output/your_output.settings | 44 ++
.../se/combined_output/your_output.unidentified | 0
.../single_indexed/se/defaults/barcodes.txt | 2 +
.../single_indexed/se/defaults/info.json | 6 +
.../single_indexed/se/defaults/input_1.fastq | 32 ++
.../se/defaults/your_output.sample_1.discarded | 4 +
.../se/defaults/your_output.sample_1.settings | 144 ++++++
.../se/defaults/your_output.sample_1.truncated | 12 +
.../se/defaults/your_output.sample_2.discarded | 4 +
.../se/defaults/your_output.sample_2.settings | 144 ++++++
.../se/defaults/your_output.sample_2.truncated | 12 +
.../se/defaults/your_output.settings | 44 ++
.../se/defaults/your_output.unidentified | 0
.../single_indexed/se/demux_only/barcodes.txt | 2 +
.../single_indexed/se/demux_only/info.json | 6 +
.../single_indexed/se/demux_only/input_1.fastq | 32 ++
.../se/demux_only/your_output.sample_1.fastq | 16 +
.../se/demux_only/your_output.sample_1.settings | 17 +
.../se/demux_only/your_output.sample_2.fastq | 16 +
.../se/demux_only/your_output.sample_2.settings | 17 +
.../se/demux_only/your_output.settings | 26 ++
.../se/demux_only/your_output.unidentified.fastq | 0
.../single_indexed/se/threads/one/barcodes.txt | 2 +
.../single_indexed/se/threads/one/info.json | 6 +
.../single_indexed/se/threads/one/input_1.fastq | 32 ++
.../se/threads/one/your_output.sample_1.discarded | 4 +
.../se/threads/one/your_output.sample_1.settings | 144 ++++++
.../se/threads/one/your_output.sample_1.truncated | 12 +
.../se/threads/one/your_output.sample_2.discarded | 4 +
.../se/threads/one/your_output.sample_2.settings | 144 ++++++
.../se/threads/one/your_output.sample_2.truncated | 12 +
.../se/threads/one/your_output.settings | 44 ++
.../se/threads/one/your_output.unidentified | 0
.../single_indexed/se/threads/three/barcodes.txt | 2 +
.../single_indexed/se/threads/three/info.json | 6 +
.../single_indexed/se/threads/three/input_1.fastq | 32 ++
.../threads/three/your_output.sample_1.discarded | 4 +
.../se/threads/three/your_output.sample_1.settings | 144 ++++++
.../threads/three/your_output.sample_1.truncated | 12 +
.../threads/three/your_output.sample_2.discarded | 4 +
.../se/threads/three/your_output.sample_2.settings | 144 ++++++
.../threads/three/your_output.sample_2.truncated | 12 +
.../se/threads/three/your_output.settings | 44 ++
.../se/threads/three/your_output.unidentified | 0
.../single_indexed/se/threads/two/barcodes.txt | 2 +
.../single_indexed/se/threads/two/info.json | 6 +
.../single_indexed/se/threads/two/input_1.fastq | 32 ++
.../se/threads/two/your_output.sample_1.discarded | 4 +
.../se/threads/two/your_output.sample_1.settings | 144 ++++++
.../se/threads/two/your_output.sample_1.truncated | 12 +
.../se/threads/two/your_output.sample_2.discarded | 4 +
.../se/threads/two/your_output.sample_2.settings | 144 ++++++
.../se/threads/two/your_output.sample_2.truncated | 12 +
.../se/threads/two/your_output.settings | 44 ++
.../se/threads/two/your_output.unidentified | 0
.../misc/bad_args/demux_without_barcodes/info.json | 7 +
.../bad_args/demux_without_barcodes/input_1.fastq | 4 +
.../bad_args/demux_without_barcodes/input_2.fastq | 4 +
validation/misc/bad_args/file2_only/info.json | 7 +
validation/misc/bad_args/file2_only/input_2.fastq | 0
validation/misc/bad_args/ident_and_demux/info.json | 7 +
.../misc/bad_args/ident_and_demux/input_1.fastq | 4 +
.../misc/bad_args/ident_and_demux/input_2.fastq | 4 +
validation/misc/bad_args/se_interleaved/info.json | 7 +
.../misc/bad_args/se_interleaved/input_1.fastq | 8 +
.../bad_args/se_interleaved/your_output.discarded | 0
.../se_interleaved/your_output.paired.truncated | 0
.../se_interleaved/your_output.singleton.truncated | 0
.../misc/bad_args/se_interleaved_input/info.json | 7 +
.../bad_args/se_interleaved_input/input_1.fastq | 8 +
.../se_interleaved_input/your_output.discarded | 0
.../your_output.pair1.truncated | 0
.../your_output.pair2.truncated | 0
.../your_output.singleton.truncated | 0
validation/misc/empty/pe/info.json | 6 +
validation/misc/empty/pe/input_1.fastq | 0
validation/misc/empty/pe/input_2.fastq | 0
validation/misc/empty/pe/your_output.discarded | 0
.../misc/empty/pe/your_output.pair1.truncated | 0
.../misc/empty/pe/your_output.pair2.truncated | 0
validation/misc/empty/pe/your_output.settings | 42 ++
.../misc/empty/pe/your_output.singleton.truncated | 0
validation/misc/empty/se/info.json | 6 +
validation/misc/empty/se/input_1.fastq | 0
validation/misc/empty/se/your_output.discarded | 0
validation/misc/empty/se/your_output.settings | 41 ++
validation/misc/empty/se/your_output.truncated | 0
validation/misc/no_arguments/info.json | 7 +
.../non_overlapping/collapse/info.json | 6 +
.../non_overlapping/collapse/input_1.fastq | 4 +
.../non_overlapping/collapse/input_2.fastq | 4 +
.../non_overlapping/collapse/your_output.collapsed | 0
.../collapse/your_output.collapsed.truncated | 0
.../non_overlapping/collapse/your_output.discarded | 0
.../collapse/your_output.pair1.truncated | 4 +
.../collapse/your_output.pair2.truncated | 4 +
.../non_overlapping/collapse/your_output.settings | 145 ++++++
.../collapse/your_output.singleton.truncated | 0
.../combined_output/collapse/info.json | 6 +
.../combined_output/collapse/input_1.fastq | 4 +
.../combined_output/collapse/input_2.fastq | 4 +
.../collapse/your_output.pair1.truncated | 4 +
.../collapse/your_output.pair2.truncated | 4 +
.../combined_output/collapse/your_output.settings | 145 ++++++
.../combined_output/interleaved/collapse/info.json | 6 +
.../interleaved/collapse/input_1.fastq | 4 +
.../interleaved/collapse/input_2.fastq | 4 +
.../collapse/your_output.paired.truncated | 8 +
.../interleaved/collapse/your_output.settings | 145 ++++++
.../interleaved/keep_both/info.json | 6 +
.../interleaved/keep_both/input_1.fastq | 4 +
.../interleaved/keep_both/input_2.fastq | 4 +
.../keep_both/your_output.paired.truncated | 8 +
.../interleaved/keep_both/your_output.settings | 143 ++++++
.../interleaved/keep_mate1/info.json | 6 +
.../interleaved/keep_mate1/input_1.fastq | 4 +
.../interleaved/keep_mate1/input_2.fastq | 4 +
.../keep_mate1/your_output.paired.truncated | 8 +
.../interleaved/keep_mate1/your_output.settings | 143 ++++++
.../interleaved/keep_mate2/info.json | 6 +
.../interleaved/keep_mate2/input_1.fastq | 4 +
.../interleaved/keep_mate2/input_2.fastq | 4 +
.../keep_mate2/your_output.paired.truncated | 8 +
.../interleaved/keep_mate2/your_output.settings | 143 ++++++
.../interleaved/keep_neither/info.json | 6 +
.../interleaved/keep_neither/input_1.fastq | 4 +
.../interleaved/keep_neither/input_2.fastq | 4 +
.../keep_neither/your_output.paired.truncated | 8 +
.../interleaved/keep_neither/your_output.settings | 142 ++++++
.../combined_output/keep_both/info.json | 6 +
.../combined_output/keep_both/input_1.fastq | 4 +
.../combined_output/keep_both/input_2.fastq | 4 +
.../keep_both/your_output.pair1.truncated | 4 +
.../keep_both/your_output.pair2.truncated | 4 +
.../combined_output/keep_both/your_output.settings | 143 ++++++
.../combined_output/keep_mate1/info.json | 6 +
.../combined_output/keep_mate1/input_1.fastq | 4 +
.../combined_output/keep_mate1/input_2.fastq | 4 +
.../keep_mate1/your_output.pair1.truncated | 4 +
.../keep_mate1/your_output.pair2.truncated | 4 +
.../keep_mate1/your_output.settings | 143 ++++++
.../combined_output/keep_mate2/info.json | 6 +
.../combined_output/keep_mate2/input_1.fastq | 4 +
.../combined_output/keep_mate2/input_2.fastq | 4 +
.../keep_mate2/your_output.pair1.truncated | 4 +
.../keep_mate2/your_output.pair2.truncated | 4 +
.../keep_mate2/your_output.settings | 143 ++++++
.../combined_output/keep_neither/info.json | 6 +
.../combined_output/keep_neither/input_1.fastq | 4 +
.../combined_output/keep_neither/input_2.fastq | 4 +
.../keep_neither/your_output.pair1.truncated | 4 +
.../keep_neither/your_output.pair2.truncated | 4 +
.../keep_neither/your_output.settings | 142 ++++++
.../non_overlapping/crlf_newlines/info.json | 6 +
.../non_overlapping/crlf_newlines/input_1.fastq | 4 +
.../non_overlapping/crlf_newlines/input_2.fastq | 4 +
.../crlf_newlines/your_output.discarded | 0
.../crlf_newlines/your_output.pair1.truncated | 4 +
.../crlf_newlines/your_output.pair2.truncated | 4 +
.../crlf_newlines/your_output.settings | 143 ++++++
.../crlf_newlines/your_output.singleton.truncated | 0
.../non_overlapping/defaults/info.json | 6 +
.../non_overlapping/defaults/input_1.fastq | 4 +
.../non_overlapping/defaults/input_2.fastq | 4 +
.../non_overlapping/defaults/your_output.discarded | 0
.../defaults/your_output.pair1.truncated | 4 +
.../defaults/your_output.pair2.truncated | 4 +
.../non_overlapping/defaults/your_output.settings | 143 ++++++
.../defaults/your_output.singleton.truncated | 0
.../non_overlapping/interleaved/both/info.json | 6 +
.../non_overlapping/interleaved/both/input_1.fastq | 8 +
.../interleaved/both/your_output.discarded | 0
.../interleaved/both/your_output.paired.truncated | 8 +
.../interleaved/both/your_output.settings | 143 ++++++
.../both/your_output.singleton.truncated | 0
.../non_overlapping/interleaved/output/info.json | 6 +
.../interleaved/output/input_1.fastq | 4 +
.../interleaved/output/input_2.fastq | 4 +
.../interleaved/output/your_output.discarded | 0
.../output/your_output.paired.truncated | 8 +
.../interleaved/output/your_output.settings | 143 ++++++
.../output/your_output.singleton.truncated | 0
.../non_overlapping/maxlength/both/info.json | 6 +
.../non_overlapping/maxlength/both/input_1.fastq | 4 +
.../non_overlapping/maxlength/both/input_2.fastq | 4 +
.../maxlength/both/your_output.discarded | 8 +
.../maxlength/both/your_output.pair1.truncated | 0
.../maxlength/both/your_output.pair2.truncated | 0
.../maxlength/both/your_output.settings | 143 ++++++
.../maxlength/both/your_output.singleton.truncated | 0
.../non_overlapping/maxlength/mate1/info.json | 6 +
.../non_overlapping/maxlength/mate1/input_1.fastq | 4 +
.../non_overlapping/maxlength/mate1/input_2.fastq | 4 +
.../maxlength/mate1/your_output.discarded | 4 +
.../maxlength/mate1/your_output.pair1.truncated | 0
.../maxlength/mate1/your_output.pair2.truncated | 0
.../maxlength/mate1/your_output.settings | 143 ++++++
.../mate1/your_output.singleton.truncated | 4 +
.../non_overlapping/maxlength/mate2/info.json | 6 +
.../non_overlapping/maxlength/mate2/input_1.fastq | 4 +
.../non_overlapping/maxlength/mate2/input_2.fastq | 4 +
.../maxlength/mate2/your_output.discarded | 4 +
.../maxlength/mate2/your_output.pair1.truncated | 0
.../maxlength/mate2/your_output.pair2.truncated | 0
.../maxlength/mate2/your_output.settings | 143 ++++++
.../mate2/your_output.singleton.truncated | 4 +
.../non_overlapping/minlength/both/info.json | 6 +
.../non_overlapping/minlength/both/input_1.fastq | 4 +
.../non_overlapping/minlength/both/input_2.fastq | 4 +
.../minlength/both/your_output.discarded | 8 +
.../minlength/both/your_output.pair1.truncated | 0
.../minlength/both/your_output.pair2.truncated | 0
.../minlength/both/your_output.settings | 86 ++++
.../minlength/both/your_output.singleton.truncated | 0
.../non_overlapping/minlength/mate1/info.json | 6 +
.../non_overlapping/minlength/mate1/input_1.fastq | 4 +
.../non_overlapping/minlength/mate1/input_2.fastq | 4 +
.../minlength/mate1/your_output.discarded | 4 +
.../minlength/mate1/your_output.pair1.truncated | 0
.../minlength/mate1/your_output.pair2.truncated | 0
.../minlength/mate1/your_output.settings | 143 ++++++
.../mate1/your_output.singleton.truncated | 4 +
.../non_overlapping/minlength/mate2/info.json | 6 +
.../non_overlapping/minlength/mate2/input_1.fastq | 4 +
.../non_overlapping/minlength/mate2/input_2.fastq | 4 +
.../minlength/mate2/your_output.discarded | 4 +
.../minlength/mate2/your_output.pair1.truncated | 0
.../minlength/mate2/your_output.pair2.truncated | 0
.../minlength/mate2/your_output.settings | 143 ++++++
.../mate2/your_output.singleton.truncated | 4 +
.../non_overlapping/trimns/excl_ns/info.json | 6 +
.../non_overlapping/trimns/excl_ns/input_1.fastq | 4 +
.../non_overlapping/trimns/excl_ns/input_2.fastq | 4 +
.../trimns/excl_ns/your_output.discarded | 0
.../trimns/excl_ns/your_output.pair1.truncated | 4 +
.../trimns/excl_ns/your_output.pair2.truncated | 4 +
.../trimns/excl_ns/your_output.settings | 143 ++++++
.../trimns/excl_ns/your_output.singleton.truncated | 0
.../non_overlapping/trimns/incl_ns/info.json | 6 +
.../non_overlapping/trimns/incl_ns/input_1.fastq | 4 +
.../non_overlapping/trimns/incl_ns/input_2.fastq | 4 +
.../trimns/incl_ns/your_output.discarded | 0
.../trimns/incl_ns/your_output.pair1.truncated | 4 +
.../trimns/incl_ns/your_output.pair2.truncated | 4 +
.../trimns/incl_ns/your_output.settings | 142 ++++++
.../trimns/incl_ns/your_output.singleton.truncated | 0
.../trimqualities/default/info.json | 6 +
.../trimqualities/default/input_1.fastq | 4 +
.../trimqualities/default/input_2.fastq | 4 +
.../trimqualities/default/your_output.discarded | 0
.../default/your_output.pair1.truncated | 4 +
.../default/your_output.pair2.truncated | 4 +
.../trimqualities/default/your_output.settings | 142 ++++++
.../default/your_output.singleton.truncated | 0
.../non_overlapping/trimqualities/minq31/info.json | 6 +
.../trimqualities/minq31/input_1.fastq | 4 +
.../trimqualities/minq31/input_2.fastq | 4 +
.../trimqualities/minq31/your_output.discarded | 0
.../minq31/your_output.pair1.truncated | 4 +
.../minq31/your_output.pair2.truncated | 4 +
.../trimqualities/minq31/your_output.settings | 111 +++++
.../minq31/your_output.singleton.truncated | 0
.../pe/excl_adapter/overlapping/collapse/info.json | 6 +
.../overlapping/collapse/input_1.fastq | 4 +
.../overlapping/collapse/input_2.fastq | 4 +
.../overlapping/collapse/your_output.collapsed | 4 +
.../collapse/your_output.collapsed.truncated | 0
.../overlapping/collapse/your_output.discarded | 0
.../collapse/your_output.pair1.truncated | 0
.../collapse/your_output.pair2.truncated | 0
.../overlapping/collapse/your_output.settings | 195 ++++++++
.../collapse/your_output.singleton.truncated | 0
.../overlapping/combined_output/collapse/info.json | 6 +
.../combined_output/collapse/input_1.fastq | 4 +
.../combined_output/collapse/input_2.fastq | 4 +
.../collapse/your_output.pair1.truncated | 4 +
.../collapse/your_output.pair2.truncated | 4 +
.../combined_output/collapse/your_output.settings | 195 ++++++++
.../combined_output/interleaved/collapse/info.json | 6 +
.../interleaved/collapse/input_1.fastq | 4 +
.../interleaved/collapse/input_2.fastq | 4 +
.../collapse/your_output.paired.truncated | 8 +
.../interleaved/collapse/your_output.settings | 195 ++++++++
.../interleaved/keep_both/info.json | 6 +
.../interleaved/keep_both/input_1.fastq | 4 +
.../interleaved/keep_both/input_2.fastq | 4 +
.../keep_both/your_output.paired.truncated | 8 +
.../interleaved/keep_both/your_output.settings | 143 ++++++
.../interleaved/keep_mate1/info.json | 6 +
.../interleaved/keep_mate1/input_1.fastq | 4 +
.../interleaved/keep_mate1/input_2.fastq | 4 +
.../keep_mate1/your_output.paired.truncated | 8 +
.../interleaved/keep_mate1/your_output.settings | 143 ++++++
.../interleaved/keep_mate2/info.json | 6 +
.../interleaved/keep_mate2/input_1.fastq | 4 +
.../interleaved/keep_mate2/input_2.fastq | 4 +
.../keep_mate2/your_output.paired.truncated | 8 +
.../interleaved/keep_mate2/your_output.settings | 143 ++++++
.../interleaved/keep_neither/info.json | 6 +
.../interleaved/keep_neither/input_1.fastq | 4 +
.../interleaved/keep_neither/input_2.fastq | 4 +
.../keep_neither/your_output.paired.truncated | 8 +
.../interleaved/keep_neither/your_output.settings | 142 ++++++
.../combined_output/keep_both/info.json | 6 +
.../combined_output/keep_both/input_1.fastq | 4 +
.../combined_output/keep_both/input_2.fastq | 4 +
.../keep_both/your_output.pair1.truncated | 4 +
.../keep_both/your_output.pair2.truncated | 4 +
.../combined_output/keep_both/your_output.settings | 143 ++++++
.../combined_output/keep_mate1/info.json | 6 +
.../combined_output/keep_mate1/input_1.fastq | 4 +
.../combined_output/keep_mate1/input_2.fastq | 4 +
.../keep_mate1/your_output.pair1.truncated | 4 +
.../keep_mate1/your_output.pair2.truncated | 4 +
.../keep_mate1/your_output.settings | 143 ++++++
.../combined_output/keep_mate2/info.json | 6 +
.../combined_output/keep_mate2/input_1.fastq | 4 +
.../combined_output/keep_mate2/input_2.fastq | 4 +
.../keep_mate2/your_output.pair1.truncated | 4 +
.../keep_mate2/your_output.pair2.truncated | 4 +
.../keep_mate2/your_output.settings | 143 ++++++
.../combined_output/keep_neither/info.json | 6 +
.../combined_output/keep_neither/input_1.fastq | 4 +
.../combined_output/keep_neither/input_2.fastq | 4 +
.../keep_neither/your_output.pair1.truncated | 4 +
.../keep_neither/your_output.pair2.truncated | 4 +
.../keep_neither/your_output.settings | 142 ++++++
.../overlapping/crlf_newlines/info.json | 6 +
.../overlapping/crlf_newlines/input_1.fastq | 4 +
.../overlapping/crlf_newlines/input_2.fastq | 4 +
.../crlf_newlines/your_output.discarded | 0
.../crlf_newlines/your_output.pair1.truncated | 4 +
.../crlf_newlines/your_output.pair2.truncated | 4 +
.../overlapping/crlf_newlines/your_output.settings | 143 ++++++
.../crlf_newlines/your_output.singleton.truncated | 0
.../pe/excl_adapter/overlapping/defaults/info.json | 6 +
.../overlapping/defaults/input_1.fastq | 4 +
.../overlapping/defaults/input_2.fastq | 4 +
.../overlapping/defaults/your_output.discarded | 0
.../defaults/your_output.pair1.truncated | 4 +
.../defaults/your_output.pair2.truncated | 4 +
.../overlapping/defaults/your_output.settings | 143 ++++++
.../defaults/your_output.singleton.truncated | 0
.../overlapping/interleaved/both/info.json | 6 +
.../overlapping/interleaved/both/input_1.fastq | 8 +
.../interleaved/both/your_output.discarded | 0
.../interleaved/both/your_output.paired.truncated | 8 +
.../interleaved/both/your_output.settings | 143 ++++++
.../both/your_output.singleton.truncated | 0
.../overlapping/interleaved/output/info.json | 6 +
.../overlapping/interleaved/output/input_1.fastq | 4 +
.../overlapping/interleaved/output/input_2.fastq | 4 +
.../interleaved/output/your_output.discarded | 0
.../output/your_output.paired.truncated | 8 +
.../interleaved/output/your_output.settings | 143 ++++++
.../output/your_output.singleton.truncated | 0
.../overlapping/maxlength/both/info.json | 6 +
.../overlapping/maxlength/both/input_1.fastq | 4 +
.../overlapping/maxlength/both/input_2.fastq | 4 +
.../maxlength/both/your_output.discarded | 8 +
.../maxlength/both/your_output.pair1.truncated | 0
.../maxlength/both/your_output.pair2.truncated | 0
.../maxlength/both/your_output.settings | 143 ++++++
.../maxlength/both/your_output.singleton.truncated | 0
.../overlapping/maxlength/mate1/info.json | 6 +
.../overlapping/maxlength/mate1/input_1.fastq | 4 +
.../overlapping/maxlength/mate1/input_2.fastq | 4 +
.../maxlength/mate1/your_output.discarded | 4 +
.../maxlength/mate1/your_output.pair1.truncated | 0
.../maxlength/mate1/your_output.pair2.truncated | 0
.../maxlength/mate1/your_output.settings | 143 ++++++
.../mate1/your_output.singleton.truncated | 4 +
.../overlapping/maxlength/mate2/info.json | 6 +
.../overlapping/maxlength/mate2/input_1.fastq | 4 +
.../overlapping/maxlength/mate2/input_2.fastq | 4 +
.../maxlength/mate2/your_output.discarded | 4 +
.../maxlength/mate2/your_output.pair1.truncated | 0
.../maxlength/mate2/your_output.pair2.truncated | 0
.../maxlength/mate2/your_output.settings | 143 ++++++
.../mate2/your_output.singleton.truncated | 4 +
.../overlapping/minlength/both/info.json | 6 +
.../overlapping/minlength/both/input_1.fastq | 4 +
.../overlapping/minlength/both/input_2.fastq | 4 +
.../minlength/both/your_output.discarded | 8 +
.../minlength/both/your_output.pair1.truncated | 0
.../minlength/both/your_output.pair2.truncated | 0
.../minlength/both/your_output.settings | 132 ++++++
.../minlength/both/your_output.singleton.truncated | 0
.../overlapping/minlength/mate1/info.json | 6 +
.../overlapping/minlength/mate1/input_1.fastq | 4 +
.../overlapping/minlength/mate1/input_2.fastq | 4 +
.../minlength/mate1/your_output.discarded | 4 +
.../minlength/mate1/your_output.pair1.truncated | 0
.../minlength/mate1/your_output.pair2.truncated | 0
.../minlength/mate1/your_output.settings | 143 ++++++
.../mate1/your_output.singleton.truncated | 4 +
.../overlapping/minlength/mate2/info.json | 6 +
.../overlapping/minlength/mate2/input_1.fastq | 4 +
.../overlapping/minlength/mate2/input_2.fastq | 4 +
.../minlength/mate2/your_output.discarded | 4 +
.../minlength/mate2/your_output.pair1.truncated | 0
.../minlength/mate2/your_output.pair2.truncated | 0
.../minlength/mate2/your_output.settings | 143 ++++++
.../mate2/your_output.singleton.truncated | 4 +
.../overlapping/trimns/excl_ns/info.json | 6 +
.../overlapping/trimns/excl_ns/input_1.fastq | 4 +
.../overlapping/trimns/excl_ns/input_2.fastq | 4 +
.../trimns/excl_ns/your_output.discarded | 0
.../trimns/excl_ns/your_output.pair1.truncated | 4 +
.../trimns/excl_ns/your_output.pair2.truncated | 4 +
.../trimns/excl_ns/your_output.settings | 143 ++++++
.../trimns/excl_ns/your_output.singleton.truncated | 0
.../overlapping/trimns/incl_ns/info.json | 6 +
.../overlapping/trimns/incl_ns/input_1.fastq | 4 +
.../overlapping/trimns/incl_ns/input_2.fastq | 4 +
.../trimns/incl_ns/your_output.discarded | 0
.../trimns/incl_ns/your_output.pair1.truncated | 4 +
.../trimns/incl_ns/your_output.pair2.truncated | 4 +
.../trimns/incl_ns/your_output.settings | 136 ++++++
.../trimns/incl_ns/your_output.singleton.truncated | 0
.../overlapping/trimqualities/default/info.json | 6 +
.../trimqualities/default/input_1.fastq | 4 +
.../trimqualities/default/input_2.fastq | 4 +
.../trimqualities/default/your_output.discarded | 0
.../default/your_output.pair1.truncated | 4 +
.../default/your_output.pair2.truncated | 4 +
.../trimqualities/default/your_output.settings | 142 ++++++
.../default/your_output.singleton.truncated | 0
.../overlapping/trimqualities/minq31/info.json | 6 +
.../overlapping/trimqualities/minq31/input_1.fastq | 4 +
.../overlapping/trimqualities/minq31/input_2.fastq | 4 +
.../trimqualities/minq31/your_output.discarded | 0
.../minq31/your_output.pair1.truncated | 4 +
.../minq31/your_output.pair2.truncated | 4 +
.../trimqualities/minq31/your_output.settings | 110 +++++
.../minq31/your_output.singleton.truncated | 0
validation/pe/incl_adapter/collapse/info.json | 6 +
validation/pe/incl_adapter/collapse/input_1.fastq | 4 +
validation/pe/incl_adapter/collapse/input_2.fastq | 4 +
.../pe/incl_adapter/collapse/your_output.collapsed | 4 +
.../collapse/your_output.collapsed.truncated | 0
.../pe/incl_adapter/collapse/your_output.discarded | 0
.../collapse/your_output.pair1.truncated | 0
.../collapse/your_output.pair2.truncated | 0
.../pe/incl_adapter/collapse/your_output.settings | 95 ++++
.../collapse/your_output.singleton.truncated | 0
.../pe/incl_adapter/collapse_truncated/info.json | 6 +
.../incl_adapter/collapse_truncated/input_1.fastq | 4 +
.../incl_adapter/collapse_truncated/input_2.fastq | 4 +
.../collapse_truncated/your_output.collapsed | 0
.../your_output.collapsed.truncated | 4 +
.../collapse_truncated/your_output.discarded | 0
.../collapse_truncated/your_output.pair1.truncated | 0
.../collapse_truncated/your_output.pair2.truncated | 0
.../collapse_truncated/your_output.settings | 94 ++++
.../your_output.singleton.truncated | 0
.../combined_output/collapse/info.json | 6 +
.../combined_output/collapse/input_1.fastq | 4 +
.../combined_output/collapse/input_2.fastq | 4 +
.../collapse/your_output.pair1.truncated | 4 +
.../collapse/your_output.pair2.truncated | 4 +
.../combined_output/collapse/your_output.settings | 95 ++++
.../combined_output/collapse_truncated/info.json | 6 +
.../collapse_truncated/input_1.fastq | 4 +
.../collapse_truncated/input_2.fastq | 4 +
.../collapse_truncated/your_output.pair1.truncated | 4 +
.../collapse_truncated/your_output.pair2.truncated | 4 +
.../collapse_truncated/your_output.settings | 94 ++++
.../combined_output/interleaved/collapse/info.json | 6 +
.../interleaved/collapse/input_1.fastq | 4 +
.../interleaved/collapse/input_2.fastq | 4 +
.../collapse/your_output.paired.truncated | 8 +
.../interleaved/collapse/your_output.settings | 95 ++++
.../interleaved/collapse_truncated/info.json | 6 +
.../interleaved/collapse_truncated/input_1.fastq | 4 +
.../interleaved/collapse_truncated/input_2.fastq | 4 +
.../your_output.paired.truncated | 8 +
.../collapse_truncated/your_output.settings | 94 ++++
.../interleaved/keep_both/info.json | 6 +
.../interleaved/keep_both/input_1.fastq | 4 +
.../interleaved/keep_both/input_2.fastq | 4 +
.../keep_both/your_output.paired.truncated | 8 +
.../interleaved/keep_both/your_output.settings | 93 ++++
.../interleaved/keep_mate1/info.json | 6 +
.../interleaved/keep_mate1/input_1.fastq | 4 +
.../interleaved/keep_mate1/input_2.fastq | 4 +
.../keep_mate1/your_output.paired.truncated | 8 +
.../interleaved/keep_mate1/your_output.settings | 93 ++++
.../interleaved/keep_mate2/info.json | 6 +
.../interleaved/keep_mate2/input_1.fastq | 4 +
.../interleaved/keep_mate2/input_2.fastq | 4 +
.../keep_mate2/your_output.paired.truncated | 8 +
.../interleaved/keep_mate2/your_output.settings | 93 ++++
.../interleaved/keep_neither/info.json | 6 +
.../interleaved/keep_neither/input_1.fastq | 4 +
.../interleaved/keep_neither/input_2.fastq | 4 +
.../keep_neither/your_output.paired.truncated | 8 +
.../interleaved/keep_neither/your_output.settings | 92 ++++
.../combined_output/keep_both/info.json | 6 +
.../combined_output/keep_both/input_1.fastq | 4 +
.../combined_output/keep_both/input_2.fastq | 4 +
.../keep_both/your_output.pair1.truncated | 4 +
.../keep_both/your_output.pair2.truncated | 4 +
.../combined_output/keep_both/your_output.settings | 93 ++++
.../combined_output/keep_mate1/info.json | 6 +
.../combined_output/keep_mate1/input_1.fastq | 4 +
.../combined_output/keep_mate1/input_2.fastq | 4 +
.../keep_mate1/your_output.pair1.truncated | 4 +
.../keep_mate1/your_output.pair2.truncated | 4 +
.../keep_mate1/your_output.settings | 93 ++++
.../combined_output/keep_mate2/info.json | 6 +
.../combined_output/keep_mate2/input_1.fastq | 4 +
.../combined_output/keep_mate2/input_2.fastq | 4 +
.../keep_mate2/your_output.pair1.truncated | 4 +
.../keep_mate2/your_output.pair2.truncated | 4 +
.../keep_mate2/your_output.settings | 93 ++++
.../combined_output/keep_neither/info.json | 6 +
.../combined_output/keep_neither/input_1.fastq | 4 +
.../combined_output/keep_neither/input_2.fastq | 4 +
.../keep_neither/your_output.pair1.truncated | 4 +
.../keep_neither/your_output.pair2.truncated | 4 +
.../keep_neither/your_output.settings | 92 ++++
validation/pe/incl_adapter/crlf_newlines/info.json | 6 +
.../pe/incl_adapter/crlf_newlines/input_1.fastq | 4 +
.../pe/incl_adapter/crlf_newlines/input_2.fastq | 4 +
.../crlf_newlines/your_output.discarded | 0
.../crlf_newlines/your_output.pair1.truncated | 4 +
.../crlf_newlines/your_output.pair2.truncated | 4 +
.../crlf_newlines/your_output.settings | 93 ++++
.../crlf_newlines/your_output.singleton.truncated | 0
validation/pe/incl_adapter/defaults/info.json | 6 +
validation/pe/incl_adapter/defaults/input_1.fastq | 4 +
validation/pe/incl_adapter/defaults/input_2.fastq | 4 +
.../pe/incl_adapter/defaults/your_output.discarded | 0
.../defaults/your_output.pair1.truncated | 4 +
.../defaults/your_output.pair2.truncated | 4 +
.../pe/incl_adapter/defaults/your_output.settings | 93 ++++
.../defaults/your_output.singleton.truncated | 0
.../pe/incl_adapter/maxlength/both/info.json | 6 +
.../pe/incl_adapter/maxlength/both/input_1.fastq | 4 +
.../pe/incl_adapter/maxlength/both/input_2.fastq | 4 +
.../maxlength/both/your_output.discarded | 8 +
.../maxlength/both/your_output.pair1.truncated | 0
.../maxlength/both/your_output.pair2.truncated | 0
.../maxlength/both/your_output.settings | 93 ++++
.../maxlength/both/your_output.singleton.truncated | 0
.../pe/incl_adapter/maxlength/mate1/info.json | 6 +
.../pe/incl_adapter/maxlength/mate1/input_1.fastq | 4 +
.../pe/incl_adapter/maxlength/mate1/input_2.fastq | 4 +
.../maxlength/mate1/your_output.discarded | 4 +
.../maxlength/mate1/your_output.pair1.truncated | 0
.../maxlength/mate1/your_output.pair2.truncated | 0
.../maxlength/mate1/your_output.settings | 93 ++++
.../mate1/your_output.singleton.truncated | 4 +
.../pe/incl_adapter/maxlength/mate2/info.json | 6 +
.../pe/incl_adapter/maxlength/mate2/input_1.fastq | 4 +
.../pe/incl_adapter/maxlength/mate2/input_2.fastq | 4 +
.../maxlength/mate2/your_output.discarded | 4 +
.../maxlength/mate2/your_output.pair1.truncated | 0
.../maxlength/mate2/your_output.pair2.truncated | 0
.../maxlength/mate2/your_output.settings | 93 ++++
.../mate2/your_output.singleton.truncated | 4 +
.../pe/incl_adapter/minlength/both/info.json | 6 +
.../pe/incl_adapter/minlength/both/input_1.fastq | 4 +
.../pe/incl_adapter/minlength/both/input_2.fastq | 4 +
.../minlength/both/your_output.discarded | 8 +
.../minlength/both/your_output.pair1.truncated | 0
.../minlength/both/your_output.pair2.truncated | 0
.../minlength/both/your_output.settings | 92 ++++
.../minlength/both/your_output.singleton.truncated | 0
.../pe/incl_adapter/minlength/mate1/info.json | 6 +
.../pe/incl_adapter/minlength/mate1/input_1.fastq | 4 +
.../pe/incl_adapter/minlength/mate1/input_2.fastq | 4 +
.../minlength/mate1/your_output.discarded | 4 +
.../minlength/mate1/your_output.pair1.truncated | 0
.../minlength/mate1/your_output.pair2.truncated | 0
.../minlength/mate1/your_output.settings | 93 ++++
.../mate1/your_output.singleton.truncated | 4 +
.../pe/incl_adapter/minlength/mate2/info.json | 6 +
.../pe/incl_adapter/minlength/mate2/input_1.fastq | 4 +
.../pe/incl_adapter/minlength/mate2/input_2.fastq | 4 +
.../minlength/mate2/your_output.discarded | 4 +
.../minlength/mate2/your_output.pair1.truncated | 0
.../minlength/mate2/your_output.pair2.truncated | 0
.../minlength/mate2/your_output.settings | 93 ++++
.../mate2/your_output.singleton.truncated | 4 +
validation/pe/incl_adapter/threads/one/info.json | 6 +
.../pe/incl_adapter/threads/one/input_1.fastq | 4 +
.../pe/incl_adapter/threads/one/input_2.fastq | 4 +
.../incl_adapter/threads/one/your_output.discarded | 0
.../threads/one/your_output.pair1.truncated | 4 +
.../threads/one/your_output.pair2.truncated | 4 +
.../incl_adapter/threads/one/your_output.settings | 93 ++++
.../threads/one/your_output.singleton.truncated | 0
validation/pe/incl_adapter/threads/three/info.json | 6 +
.../pe/incl_adapter/threads/three/input_1.fastq | 4 +
.../pe/incl_adapter/threads/three/input_2.fastq | 4 +
.../threads/three/your_output.discarded | 0
.../threads/three/your_output.pair1.truncated | 4 +
.../threads/three/your_output.pair2.truncated | 4 +
.../threads/three/your_output.settings | 93 ++++
.../threads/three/your_output.singleton.truncated | 0
validation/pe/incl_adapter/threads/two/info.json | 6 +
.../pe/incl_adapter/threads/two/input_1.fastq | 4 +
.../pe/incl_adapter/threads/two/input_2.fastq | 4 +
.../incl_adapter/threads/two/your_output.discarded | 0
.../threads/two/your_output.pair1.truncated | 4 +
.../threads/two/your_output.pair2.truncated | 4 +
.../incl_adapter/threads/two/your_output.settings | 93 ++++
.../threads/two/your_output.singleton.truncated | 0
.../pe/incl_adapter/trimns/excl_ns/info.json | 6 +
.../pe/incl_adapter/trimns/excl_ns/input_1.fastq | 4 +
.../pe/incl_adapter/trimns/excl_ns/input_2.fastq | 4 +
.../trimns/excl_ns/your_output.discarded | 0
.../trimns/excl_ns/your_output.pair1.truncated | 4 +
.../trimns/excl_ns/your_output.pair2.truncated | 4 +
.../trimns/excl_ns/your_output.settings | 93 ++++
.../trimns/excl_ns/your_output.singleton.truncated | 0
.../pe/incl_adapter/trimns/incl_ns/info.json | 6 +
.../pe/incl_adapter/trimns/incl_ns/input_1.fastq | 4 +
.../pe/incl_adapter/trimns/incl_ns/input_2.fastq | 4 +
.../trimns/incl_ns/your_output.discarded | 0
.../trimns/incl_ns/your_output.pair1.truncated | 4 +
.../trimns/incl_ns/your_output.pair2.truncated | 4 +
.../trimns/incl_ns/your_output.settings | 92 ++++
.../trimns/incl_ns/your_output.singleton.truncated | 0
.../incl_adapter/trimqualities/default/info.json | 6 +
.../trimqualities/default/input_1.fastq | 4 +
.../trimqualities/default/input_2.fastq | 4 +
.../trimqualities/default/your_output.discarded | 0
.../default/your_output.pair1.truncated | 4 +
.../default/your_output.pair2.truncated | 4 +
.../trimqualities/default/your_output.settings | 93 ++++
.../default/your_output.singleton.truncated | 0
.../pe/incl_adapter/trimqualities/minq35/info.json | 6 +
.../trimqualities/minq35/input_1.fastq | 4 +
.../trimqualities/minq35/input_2.fastq | 4 +
.../trimqualities/minq35/your_output.discarded | 0
.../minq35/your_output.pair1.truncated | 4 +
.../minq35/your_output.pair2.truncated | 4 +
.../trimqualities/minq35/your_output.settings | 92 ++++
.../minq35/your_output.singleton.truncated | 0
validation/pe/only_adapter/collapse/info.json | 6 +
validation/pe/only_adapter/collapse/input_1.fastq | 4 +
validation/pe/only_adapter/collapse/input_2.fastq | 4 +
.../pe/only_adapter/collapse/your_output.collapsed | 0
.../collapse/your_output.collapsed.truncated | 0
.../pe/only_adapter/collapse/your_output.discarded | 4 +
.../collapse/your_output.pair1.truncated | 0
.../collapse/your_output.pair2.truncated | 0
.../pe/only_adapter/collapse/your_output.settings | 45 ++
.../collapse/your_output.singleton.truncated | 0
.../combined_output/collapse/info.json | 6 +
.../combined_output/collapse/input_1.fastq | 4 +
.../combined_output/collapse/input_2.fastq | 4 +
.../collapse/your_output.pair1.truncated | 4 +
.../collapse/your_output.pair2.truncated | 4 +
.../combined_output/collapse/your_output.settings | 45 ++
.../combined_output/defaults/info.json | 6 +
.../combined_output/defaults/input_1.fastq | 4 +
.../combined_output/defaults/input_2.fastq | 4 +
.../defaults/your_output.pair1.truncated | 4 +
.../defaults/your_output.pair2.truncated | 4 +
.../combined_output/defaults/your_output.settings | 43 ++
validation/pe/only_adapter/crlf_newlines/info.json | 6 +
.../pe/only_adapter/crlf_newlines/input_1.fastq | 4 +
.../pe/only_adapter/crlf_newlines/input_2.fastq | 4 +
.../crlf_newlines/your_output.discarded | 8 +
.../crlf_newlines/your_output.pair1.truncated | 0
.../crlf_newlines/your_output.pair2.truncated | 0
.../crlf_newlines/your_output.settings | 43 ++
.../crlf_newlines/your_output.singleton.truncated | 0
validation/pe/only_adapter/defaults/info.json | 6 +
validation/pe/only_adapter/defaults/input_1.fastq | 4 +
validation/pe/only_adapter/defaults/input_2.fastq | 4 +
.../pe/only_adapter/defaults/your_output.discarded | 8 +
.../defaults/your_output.pair1.truncated | 0
.../defaults/your_output.pair2.truncated | 0
.../pe/only_adapter/defaults/your_output.settings | 43 ++
.../defaults/your_output.singleton.truncated | 0
validation/pe/only_adapter/minlength/info.json | 6 +
validation/pe/only_adapter/minlength/input_1.fastq | 4 +
validation/pe/only_adapter/minlength/input_2.fastq | 4 +
.../only_adapter/minlength/your_output.discarded | 0
.../minlength/your_output.pair1.truncated | 4 +
.../minlength/your_output.pair2.truncated | 4 +
.../pe/only_adapter/minlength/your_output.settings | 43 ++
.../minlength/your_output.singleton.truncated | 0
validation/run | 498 +++++++++++++++++++++
validation/se/excl_adapter/collapse/info.json | 6 +
validation/se/excl_adapter/collapse/input_1.fastq | 4 +
.../se/excl_adapter/collapse/your_output.collapsed | 0
.../collapse/your_output.collapsed.truncated | 0
.../se/excl_adapter/collapse/your_output.discarded | 0
.../se/excl_adapter/collapse/your_output.settings | 144 ++++++
.../se/excl_adapter/collapse/your_output.truncated | 4 +
.../combined_output/collapse/info.json | 6 +
.../combined_output/collapse/input_1.fastq | 4 +
.../combined_output/collapse/your_output.settings | 144 ++++++
.../combined_output/collapse/your_output.truncated | 4 +
.../combined_output/discarded/info.json | 6 +
.../combined_output/discarded/input_1.fastq | 4 +
.../combined_output/discarded/your_output.settings | 142 ++++++
.../discarded/your_output.truncated | 4 +
.../combined_output/retained/info.json | 6 +
.../combined_output/retained/input_1.fastq | 4 +
.../combined_output/retained/your_output.settings | 142 ++++++
.../combined_output/retained/your_output.truncated | 4 +
validation/se/excl_adapter/crlf_newlines/info.json | 6 +
.../se/excl_adapter/crlf_newlines/input_1.fastq | 4 +
.../crlf_newlines/your_output.discarded | 0
.../crlf_newlines/your_output.settings | 142 ++++++
.../crlf_newlines/your_output.truncated | 4 +
validation/se/excl_adapter/defaults/info.json | 6 +
validation/se/excl_adapter/defaults/input_1.fastq | 4 +
.../se/excl_adapter/defaults/your_output.discarded | 0
.../se/excl_adapter/defaults/your_output.settings | 142 ++++++
.../se/excl_adapter/defaults/your_output.truncated | 4 +
validation/se/excl_adapter/maxlength/info.json | 6 +
validation/se/excl_adapter/maxlength/input_1.fastq | 4 +
.../excl_adapter/maxlength/your_output.discarded | 4 +
.../se/excl_adapter/maxlength/your_output.settings | 142 ++++++
.../excl_adapter/maxlength/your_output.truncated | 0
validation/se/excl_adapter/minlength/info.json | 6 +
validation/se/excl_adapter/minlength/input_1.fastq | 4 +
.../excl_adapter/minlength/your_output.discarded | 4 +
.../se/excl_adapter/minlength/your_output.settings | 142 ++++++
.../excl_adapter/minlength/your_output.truncated | 0
.../se/excl_adapter/trimns/excl_ns/info.json | 6 +
.../se/excl_adapter/trimns/excl_ns/input_1.fastq | 4 +
.../trimns/excl_ns/your_output.discarded | 0
.../trimns/excl_ns/your_output.settings | 142 ++++++
.../trimns/excl_ns/your_output.truncated | 4 +
.../se/excl_adapter/trimns/incl_ns/info.json | 6 +
.../se/excl_adapter/trimns/incl_ns/input_1.fastq | 4 +
.../trimns/incl_ns/your_output.discarded | 0
.../trimns/incl_ns/your_output.settings | 136 ++++++
.../trimns/incl_ns/your_output.truncated | 4 +
.../excl_adapter/trimqualities/default/info.json | 6 +
.../trimqualities/default/input_1.fastq | 4 +
.../trimqualities/default/your_output.discarded | 0
.../trimqualities/default/your_output.settings | 141 ++++++
.../trimqualities/default/your_output.truncated | 4 +
.../se/excl_adapter/trimqualities/minq31/info.json | 6 +
.../trimqualities/minq31/input_1.fastq | 4 +
.../trimqualities/minq31/your_output.discarded | 0
.../trimqualities/minq31/your_output.settings | 109 +++++
.../trimqualities/minq31/your_output.truncated | 4 +
validation/se/incl_adapter/collapse/info.json | 6 +
validation/se/incl_adapter/collapse/input_1.fastq | 4 +
.../se/incl_adapter/collapse/your_output.collapsed | 4 +
.../collapse/your_output.collapsed.truncated | 0
.../se/incl_adapter/collapse/your_output.discarded | 0
.../se/incl_adapter/collapse/your_output.settings | 94 ++++
.../se/incl_adapter/collapse/your_output.truncated | 0
.../se/incl_adapter/collapse_truncated/info.json | 6 +
.../incl_adapter/collapse_truncated/input_1.fastq | 4 +
.../collapse_truncated/your_output.collapsed | 0
.../your_output.collapsed.truncated | 4 +
.../collapse_truncated/your_output.discarded | 0
.../collapse_truncated/your_output.settings | 93 ++++
.../collapse_truncated/your_output.truncated | 0
.../combined_output/collapse/info.json | 6 +
.../combined_output/collapse/input_1.fastq | 4 +
.../combined_output/collapse/your_output.settings | 94 ++++
.../combined_output/collapse/your_output.truncated | 4 +
.../combined_output/collapse_truncated/info.json | 6 +
.../collapse_truncated/input_1.fastq | 4 +
.../collapse_truncated/your_output.settings | 93 ++++
.../collapse_truncated/your_output.truncated | 4 +
.../combined_output/discarded/info.json | 6 +
.../combined_output/discarded/input_1.fastq | 4 +
.../combined_output/discarded/your_output.settings | 92 ++++
.../discarded/your_output.truncated | 4 +
.../combined_output/retained/info.json | 6 +
.../combined_output/retained/input_1.fastq | 4 +
.../combined_output/retained/your_output.settings | 92 ++++
.../combined_output/retained/your_output.truncated | 4 +
validation/se/incl_adapter/crlf_newlines/info.json | 6 +
.../se/incl_adapter/crlf_newlines/input_1.fastq | 4 +
.../crlf_newlines/your_output.discarded | 0
.../crlf_newlines/your_output.settings | 92 ++++
.../crlf_newlines/your_output.truncated | 4 +
validation/se/incl_adapter/defaults/info.json | 6 +
validation/se/incl_adapter/defaults/input_1.fastq | 4 +
.../se/incl_adapter/defaults/your_output.discarded | 0
.../se/incl_adapter/defaults/your_output.settings | 92 ++++
.../se/incl_adapter/defaults/your_output.truncated | 4 +
validation/se/incl_adapter/maxlength/info.json | 6 +
validation/se/incl_adapter/maxlength/input_1.fastq | 4 +
.../incl_adapter/maxlength/your_output.discarded | 4 +
.../se/incl_adapter/maxlength/your_output.settings | 92 ++++
.../incl_adapter/maxlength/your_output.truncated | 0
validation/se/incl_adapter/minlength/info.json | 6 +
validation/se/incl_adapter/minlength/input_1.fastq | 4 +
.../incl_adapter/minlength/your_output.discarded | 4 +
.../se/incl_adapter/minlength/your_output.settings | 92 ++++
.../incl_adapter/minlength/your_output.truncated | 0
validation/se/incl_adapter/threads/one/info.json | 6 +
.../se/incl_adapter/threads/one/input_1.fastq | 4 +
.../incl_adapter/threads/one/your_output.discarded | 0
.../incl_adapter/threads/one/your_output.settings | 92 ++++
.../incl_adapter/threads/one/your_output.truncated | 4 +
validation/se/incl_adapter/threads/three/info.json | 6 +
.../se/incl_adapter/threads/three/input_1.fastq | 4 +
.../threads/three/your_output.discarded | 0
.../threads/three/your_output.settings | 92 ++++
.../threads/three/your_output.truncated | 4 +
validation/se/incl_adapter/threads/two/info.json | 6 +
.../se/incl_adapter/threads/two/input_1.fastq | 4 +
.../incl_adapter/threads/two/your_output.discarded | 0
.../incl_adapter/threads/two/your_output.settings | 92 ++++
.../incl_adapter/threads/two/your_output.truncated | 4 +
.../se/incl_adapter/trimns/excl_ns/info.json | 6 +
.../se/incl_adapter/trimns/excl_ns/input_1.fastq | 4 +
.../trimns/excl_ns/your_output.discarded | 0
.../trimns/excl_ns/your_output.settings | 92 ++++
.../trimns/excl_ns/your_output.truncated | 4 +
.../se/incl_adapter/trimns/incl_ns/info.json | 6 +
.../se/incl_adapter/trimns/incl_ns/input_1.fastq | 4 +
.../trimns/incl_ns/your_output.discarded | 0
.../trimns/incl_ns/your_output.settings | 86 ++++
.../trimns/incl_ns/your_output.truncated | 4 +
.../incl_adapter/trimqualities/default/info.json | 6 +
.../trimqualities/default/input_1.fastq | 4 +
.../trimqualities/default/your_output.discarded | 0
.../trimqualities/default/your_output.settings | 92 ++++
.../trimqualities/default/your_output.truncated | 4 +
.../se/incl_adapter/trimqualities/minq36/info.json | 6 +
.../trimqualities/minq36/input_1.fastq | 4 +
.../trimqualities/minq36/your_output.discarded | 0
.../trimqualities/minq36/your_output.settings | 87 ++++
.../trimqualities/minq36/your_output.truncated | 4 +
validation/se/only_adapter/collapse/info.json | 6 +
validation/se/only_adapter/collapse/input_1.fastq | 4 +
.../se/only_adapter/collapse/your_output.collapsed | 0
.../collapse/your_output.collapsed.truncated | 0
.../se/only_adapter/collapse/your_output.discarded | 4 +
.../se/only_adapter/collapse/your_output.settings | 44 ++
.../se/only_adapter/collapse/your_output.truncated | 0
.../combined_output/discarded/info.json | 6 +
.../combined_output/discarded/input_1.fastq | 4 +
.../combined_output/discarded/your_output.settings | 42 ++
.../discarded/your_output.truncated | 4 +
.../combined_output/retained/info.json | 6 +
.../combined_output/retained/input_1.fastq | 4 +
.../combined_output/retained/your_output.settings | 42 ++
.../combined_output/retained/your_output.truncated | 4 +
validation/se/only_adapter/crlf_newlines/info.json | 6 +
.../se/only_adapter/crlf_newlines/input_1.fastq | 4 +
.../crlf_newlines/your_output.discarded | 4 +
.../crlf_newlines/your_output.settings | 42 ++
.../crlf_newlines/your_output.truncated | 0
validation/se/only_adapter/defaults/info.json | 6 +
validation/se/only_adapter/defaults/input_1.fastq | 4 +
.../se/only_adapter/defaults/your_output.discarded | 4 +
.../se/only_adapter/defaults/your_output.settings | 42 ++
.../se/only_adapter/defaults/your_output.truncated | 0
validation/se/only_adapter/minlength/info.json | 6 +
validation/se/only_adapter/minlength/input_1.fastq | 4 +
.../only_adapter/minlength/your_output.discarded | 0
.../se/only_adapter/minlength/your_output.settings | 42 ++
.../only_adapter/minlength/your_output.truncated | 4 +
1319 files changed, 32585 insertions(+), 1409 deletions(-)
create mode 100644 examples/Makefile
create mode 100644 src/main_demultiplex.cc
create mode 100644 src/trimmed_reads.cc
create mode 100644 src/trimmed_reads.h
create mode 100644 validation/README
create mode 100644 validation/demultiplexing/double_indexed/pe/collapse/barcodes.txt
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create mode 100644 validation/demultiplexing/double_indexed/pe/defaults/barcodes.txt
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create mode 100644 validation/demultiplexing/double_indexed/pe/defaults/your_output.sample_1.discarded
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create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/interleaved/barcodes.txt
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create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_1.paired.fastq
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create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.paired.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.sample_2.settings
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.settings
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/interleaved/your_output.unidentified.paired.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/barcodes.txt
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/info.json
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/input_1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/input_2.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.pair2.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_1.settings
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.pair2.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.sample_2.settings
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.settings
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.unidentified_1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/regular/your_output.unidentified_2.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/barcodes.txt
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/info.json
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/input_2.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.pair2.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_1.settings
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.pair2.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.sample_2.settings
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.settings
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/demux_only/unidentified/your_output.unidentified_2.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/interleaved/both/barcodes.txt
create mode 100644 validation/demultiplexing/double_indexed/pe/interleaved/both/info.json
create mode 100644 validation/demultiplexing/double_indexed/pe/interleaved/both/input_1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/interleaved/both/your_output.sample_1.discarded
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create mode 100644 validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_1.discarded
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create mode 100644 validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.sample_2.settings
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create mode 100644 validation/demultiplexing/double_indexed/pe/interleaved/output/your_output.unidentified.paired
create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/barcodes.txt
create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/info.json
create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/input_1.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/input_2.fastq
create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.discarded
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create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.pair2.truncated
create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_1.settings
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create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/your_output.sample_2.settings
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create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/your_output.unidentified_1
create mode 100644 validation/demultiplexing/double_indexed/pe/threads/one/your_output.unidentified_2
create mode 100644 validation/demultiplexing/double_indexed/pe/threads/three/barcodes.txt
create mode 100644 validation/demultiplexing/double_indexed/pe/threads/three/info.json
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create mode 100644 validation/demultiplexing/double_indexed/pe/threads/two/barcodes.txt
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create mode 100644 validation/se/incl_adapter/maxlength/input_1.fastq
create mode 100644 validation/se/incl_adapter/maxlength/your_output.discarded
create mode 100644 validation/se/incl_adapter/maxlength/your_output.settings
create mode 100644 validation/se/incl_adapter/maxlength/your_output.truncated
create mode 100644 validation/se/incl_adapter/minlength/info.json
create mode 100644 validation/se/incl_adapter/minlength/input_1.fastq
create mode 100644 validation/se/incl_adapter/minlength/your_output.discarded
create mode 100644 validation/se/incl_adapter/minlength/your_output.settings
create mode 100644 validation/se/incl_adapter/minlength/your_output.truncated
create mode 100644 validation/se/incl_adapter/threads/one/info.json
create mode 100644 validation/se/incl_adapter/threads/one/input_1.fastq
create mode 100644 validation/se/incl_adapter/threads/one/your_output.discarded
create mode 100644 validation/se/incl_adapter/threads/one/your_output.settings
create mode 100644 validation/se/incl_adapter/threads/one/your_output.truncated
create mode 100644 validation/se/incl_adapter/threads/three/info.json
create mode 100644 validation/se/incl_adapter/threads/three/input_1.fastq
create mode 100644 validation/se/incl_adapter/threads/three/your_output.discarded
create mode 100644 validation/se/incl_adapter/threads/three/your_output.settings
create mode 100644 validation/se/incl_adapter/threads/three/your_output.truncated
create mode 100644 validation/se/incl_adapter/threads/two/info.json
create mode 100644 validation/se/incl_adapter/threads/two/input_1.fastq
create mode 100644 validation/se/incl_adapter/threads/two/your_output.discarded
create mode 100644 validation/se/incl_adapter/threads/two/your_output.settings
create mode 100644 validation/se/incl_adapter/threads/two/your_output.truncated
create mode 100644 validation/se/incl_adapter/trimns/excl_ns/info.json
create mode 100644 validation/se/incl_adapter/trimns/excl_ns/input_1.fastq
create mode 100644 validation/se/incl_adapter/trimns/excl_ns/your_output.discarded
create mode 100644 validation/se/incl_adapter/trimns/excl_ns/your_output.settings
create mode 100644 validation/se/incl_adapter/trimns/excl_ns/your_output.truncated
create mode 100644 validation/se/incl_adapter/trimns/incl_ns/info.json
create mode 100644 validation/se/incl_adapter/trimns/incl_ns/input_1.fastq
create mode 100644 validation/se/incl_adapter/trimns/incl_ns/your_output.discarded
create mode 100644 validation/se/incl_adapter/trimns/incl_ns/your_output.settings
create mode 100644 validation/se/incl_adapter/trimns/incl_ns/your_output.truncated
create mode 100644 validation/se/incl_adapter/trimqualities/default/info.json
create mode 100644 validation/se/incl_adapter/trimqualities/default/input_1.fastq
create mode 100644 validation/se/incl_adapter/trimqualities/default/your_output.discarded
create mode 100644 validation/se/incl_adapter/trimqualities/default/your_output.settings
create mode 100644 validation/se/incl_adapter/trimqualities/default/your_output.truncated
create mode 100644 validation/se/incl_adapter/trimqualities/minq36/info.json
create mode 100644 validation/se/incl_adapter/trimqualities/minq36/input_1.fastq
create mode 100644 validation/se/incl_adapter/trimqualities/minq36/your_output.discarded
create mode 100644 validation/se/incl_adapter/trimqualities/minq36/your_output.settings
create mode 100644 validation/se/incl_adapter/trimqualities/minq36/your_output.truncated
create mode 100644 validation/se/only_adapter/collapse/info.json
create mode 100644 validation/se/only_adapter/collapse/input_1.fastq
create mode 100644 validation/se/only_adapter/collapse/your_output.collapsed
create mode 100644 validation/se/only_adapter/collapse/your_output.collapsed.truncated
create mode 100644 validation/se/only_adapter/collapse/your_output.discarded
create mode 100644 validation/se/only_adapter/collapse/your_output.settings
create mode 100644 validation/se/only_adapter/collapse/your_output.truncated
create mode 100644 validation/se/only_adapter/combined_output/discarded/info.json
create mode 100644 validation/se/only_adapter/combined_output/discarded/input_1.fastq
create mode 100644 validation/se/only_adapter/combined_output/discarded/your_output.settings
create mode 100644 validation/se/only_adapter/combined_output/discarded/your_output.truncated
create mode 100644 validation/se/only_adapter/combined_output/retained/info.json
create mode 100644 validation/se/only_adapter/combined_output/retained/input_1.fastq
create mode 100644 validation/se/only_adapter/combined_output/retained/your_output.settings
create mode 100644 validation/se/only_adapter/combined_output/retained/your_output.truncated
create mode 100644 validation/se/only_adapter/crlf_newlines/info.json
create mode 100644 validation/se/only_adapter/crlf_newlines/input_1.fastq
create mode 100644 validation/se/only_adapter/crlf_newlines/your_output.discarded
create mode 100644 validation/se/only_adapter/crlf_newlines/your_output.settings
create mode 100644 validation/se/only_adapter/crlf_newlines/your_output.truncated
create mode 100644 validation/se/only_adapter/defaults/info.json
create mode 100644 validation/se/only_adapter/defaults/input_1.fastq
create mode 100644 validation/se/only_adapter/defaults/your_output.discarded
create mode 100644 validation/se/only_adapter/defaults/your_output.settings
create mode 100644 validation/se/only_adapter/defaults/your_output.truncated
create mode 100644 validation/se/only_adapter/minlength/info.json
create mode 100644 validation/se/only_adapter/minlength/input_1.fastq
create mode 100644 validation/se/only_adapter/minlength/your_output.discarded
create mode 100644 validation/se/only_adapter/minlength/your_output.settings
create mode 100644 validation/se/only_adapter/minlength/your_output.truncated
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