data/atropos-1.1.24+dfsg/.dockerignore: ASCII text data/atropos-1.1.24+dfsg/.gitattributes: ASCII text data/atropos-1.1.24+dfsg/.gitignore: ASCII text data/atropos-1.1.24+dfsg/.pylintrc: ASCII text data/atropos-1.1.24+dfsg/.travis.yml: ASCII text, with very long lines data/atropos-1.1.24+dfsg/CHANGES.md: ASCII text, with very long lines data/atropos-1.1.24+dfsg/CITATION: ASCII text data/atropos-1.1.24+dfsg/CODE_OF_CONDUCT.md: ASCII text data/atropos-1.1.24+dfsg/CONTRIBUTING.md: ASCII text data/atropos-1.1.24+dfsg/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/LICENSE: ASCII text data/atropos-1.1.24+dfsg/MANIFEST.in: ASCII text data/atropos-1.1.24+dfsg/Makefile: makefile script, ASCII text data/atropos-1.1.24+dfsg/README.md: UTF-8 Unicode text, with very long lines data/atropos-1.1.24+dfsg/atropos/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/_version.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/adapters/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/adapters/sequencing_adapters.fa: ASCII text data/atropos-1.1.24+dfsg/atropos/align/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/align/_align.pyx: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/base.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/cli.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/detect/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/detect/cli.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/detect/reports.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/error/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/error/cli.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/error/reports.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/legacy_report.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/multicore.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/qc/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/qc/cli.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/qc/reports.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/reports.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/stats.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/trim/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/trim/_qualtrim.pyx: ASCII text data/atropos-1.1.24+dfsg/atropos/commands/trim/cli.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/trim/filters.py: Python script, UTF-8 Unicode text executable data/atropos-1.1.24+dfsg/atropos/commands/trim/modifiers.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/trim/multicore.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/trim/qualtrim.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/trim/reports.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/commands/trim/writers.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/io/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/io/_seqio.pyx: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/io/compression.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/io/progress.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/io/seqio.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/util/__init__.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/atropos/util/colorspace.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/bin/_preamble.py: ASCII text data/atropos-1.1.24+dfsg/bin/atropos: Python script, ASCII text executable data/atropos-1.1.24+dfsg/doc/Makefile: makefile script, ASCII text, with very long lines data/atropos-1.1.24+dfsg/doc/_static/adapters.svg: SVG Scalable Vector Graphics image data/atropos-1.1.24+dfsg/doc/_static/logo.svg: SVG Scalable Vector Graphics image data/atropos-1.1.24+dfsg/doc/colorspace.rst: UTF-8 Unicode text data/atropos-1.1.24+dfsg/doc/conf.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/doc/developers.rst: ASCII text data/atropos-1.1.24+dfsg/doc/guide.rst: UTF-8 Unicode text data/atropos-1.1.24+dfsg/doc/index.rst: ASCII text data/atropos-1.1.24+dfsg/doc/installation.rst: ASCII text data/atropos-1.1.24+dfsg/doc/logo.ai: PDF document, version 1.5 data/atropos-1.1.24+dfsg/doc/recipes.rst: ASCII text data/atropos-1.1.24+dfsg/meta.yaml: ASCII text data/atropos-1.1.24+dfsg/paper/README.md: ASCII text, with very long lines data/atropos-1.1.24+dfsg/paper/containers/README.md: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/DataSets.xlsx: Microsoft Excel 2007+ data/atropos-1.1.24+dfsg/paper/containers/data/README.md: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg37/bwa-index/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg37/bwa-index/build.sh: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg37/bwameth-index/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg37/bwameth-index/build.sh: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg37/reference/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg37/reference/build.sh: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg37/star-index/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg37/star-index/build.sh: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg38/bwa-index/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg38/bwa-index/build.sh: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg38/bwameth-index/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg38/bwameth-index/build.sh: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg38/reference/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg38/reference/build.sh: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg38/star-index/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/hg38/star-index/build.sh: Bourne-Again shell script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/data/rna/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/rna/build.sh: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/adjust_error_profiles.R: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/art_profiles.txt: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/art_profiles/HiSeq2500L125R1_001.txt: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/art_profiles/HiSeq2500L125R1_005.txt: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/art_profiles/HiSeq2500L125R1_01.txt: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/art_profiles/HiSeq2500L125R2_001.txt: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/art_profiles/HiSeq2500L125R2_005.txt: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/art_profiles/HiSeq2500L125R2_01.txt: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/simulated/build.sh: Bourne-Again shell script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/data/wgbs/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/data/wgbs/build.sh: Bourne-Again shell script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/docker2singularity.sh: Bourne-Again shell script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/paper_containers.txt: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/README.md: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/adapter-removal/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/adapter-removal/adapter-removal.cwl: a /usr/bin/env cwl-runner script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/art/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/atropos-paper-analysis/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/atropos-paper-analysis/fastq-dump-wrapper.sh: Bourne-Again shell script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/atropos-paper/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/atropos-paper/atropos.cwl: a /usr/bin/env cwl-runner script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/bwa/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/bwa/README.md: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/bwa/bwamem.cwl: a /usr/bin/env cwl-runner script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/bwa/bwameth.cwl: a /usr/bin/env cwl-runner script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/cutadapt/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/cutadapt/cutadapt.cwl: a /usr/bin/env cwl-runner script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/fastp/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/fastp/fastp.cwl: a /usr/bin/env cwl-runner script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/python-bash/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/seqpurge/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/seqpurge/seqpurge.cwl: a /usr/bin/env cwl-runner script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/skewer/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/skewer/skewer.cwl: a /usr/bin/env cwl-runner script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/star/Dockerfile: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/star/README.md: ASCII text data/atropos-1.1.24+dfsg/paper/containers/tools/star/star.cwl: a /usr/bin/env cwl-runner script, ASCII text executable data/atropos-1.1.24+dfsg/paper/containers/tools/tool-names.txt: ASCII text data/atropos-1.1.24+dfsg/paper/manuscript/README.md: ASCII text data/atropos-1.1.24+dfsg/paper/manuscript/citations.bib: BibTeX text file, UTF-8 Unicode text, with very long lines data/atropos-1.1.24+dfsg/paper/manuscript/main/figures/Figure1.graffle: gzip compressed data, from FAT filesystem (MS-DOS, OS/2, NT), original size modulo 2^32 99273 data/atropos-1.1.24+dfsg/paper/manuscript/main/figures/Figure1.pdf: PDF document, version 1.3 data/atropos-1.1.24+dfsg/paper/manuscript/main/figures/Figure2.pdf: PDF document, version 1.5 data/atropos-1.1.24+dfsg/paper/manuscript/main/figures/Figure3.pdf: PDF document, version 1.5 data/atropos-1.1.24+dfsg/paper/manuscript/main/figures/Figure4.pdf: PDF document, version 1.5 data/atropos-1.1.24+dfsg/paper/manuscript/main/figures/Figure5.pdf: PDF document, version 1.5 data/atropos-1.1.24+dfsg/paper/manuscript/main/tex/datasets_table.tex: LaTeX document, ASCII text, with very long lines data/atropos-1.1.24+dfsg/paper/manuscript/main/tex/main.tex: LaTeX 2e document, UTF-8 Unicode text, with very long lines data/atropos-1.1.24+dfsg/paper/manuscript/main/tex/simulated_accuracy_table.tex: LaTeX document, ASCII text, with very long lines data/atropos-1.1.24+dfsg/paper/manuscript/pdfs/manuscript.pdf: PDF document, version 1.3 data/atropos-1.1.24+dfsg/paper/manuscript/pdfs/response.pdf: PDF document, version 1.5 data/atropos-1.1.24+dfsg/paper/manuscript/pdfs/supplement.pdf: PDF document, version 1.5 data/atropos-1.1.24+dfsg/paper/manuscript/supplement/figures/FigureS1.pdf: PDF document, version 1.5 data/atropos-1.1.24+dfsg/paper/manuscript/supplement/figures/FigureS2.pdf: PDF document, version 1.5 data/atropos-1.1.24+dfsg/paper/manuscript/supplement/figures/FigureS3.pdf: PDF document, version 1.5 data/atropos-1.1.24+dfsg/paper/manuscript/supplement/tex/TableS1.tex: LaTeX document, ASCII text data/atropos-1.1.24+dfsg/paper/manuscript/supplement/tex/TableS2.tex: LaTeX document, ASCII text data/atropos-1.1.24+dfsg/paper/manuscript/supplement/tex/TableS3.tex: LaTeX document, ASCII text data/atropos-1.1.24+dfsg/paper/manuscript/supplement/tex/TableS4.tex: LaTeX document, ASCII text data/atropos-1.1.24+dfsg/paper/manuscript/supplement/tex/TableS5.tex: LaTeX document, ASCII text data/atropos-1.1.24+dfsg/paper/manuscript/supplement/tex/TableS6.tex: LaTeX document, ASCII text data/atropos-1.1.24+dfsg/paper/manuscript/supplement/tex/main.tex: LaTeX 2e document, ASCII text, with very long lines data/atropos-1.1.24+dfsg/paper/manuscript/wlpeerj.cls: LaTeX document, ASCII text data/atropos-1.1.24+dfsg/paper/workflow/bin/common.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/compute_real_effectiveness.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/compute_simulated_accuracy.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/job_memory_table.tex: LaTeX document, ASCII text data/atropos-1.1.24+dfsg/paper/workflow/bin/parse_gtime.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/parse_machine.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/parse_slurm_job.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/performance_table.tex: LaTeX document, ASCII text data/atropos-1.1.24+dfsg/paper/workflow/bin/show_job_info.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/show_performance.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/show_rnaseq_effectiveness.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/show_simulated_accuracy.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/show_wgbs_effectiveness.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/simulated_accuracy_table.tex: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/bin/summarize_slurm_job.sh: Bourne-Again shell script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/extra/estimate_real_data_metrics.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/extra/fastq_base_hist.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/extra/perftest.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/nextflow.config: ASCII text data/atropos-1.1.24+dfsg/paper/workflow/rnaseq.nf: a /usr/bin/env nextflow script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/run-workflows.sh: Bourne-Again shell script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/simulated.nf: a /usr/bin/env nextflow script, ASCII text executable data/atropos-1.1.24+dfsg/paper/workflow/wgbs.nf: a /usr/bin/env nextflow script, ASCII text executable data/atropos-1.1.24+dfsg/pytest.ini: ASCII text data/atropos-1.1.24+dfsg/setup.cfg: Windows setup INFormation data/atropos-1.1.24+dfsg/setup.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/.gitignore: ASCII text data/atropos-1.1.24+dfsg/tests/__init__.py: empty data/atropos-1.1.24+dfsg/tests/cut/454.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/SRR2040662_trimmed.fq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/anchored-back.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/anchored.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/anchored_no_indels.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/anchored_no_indels_wildcard.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/anywhere_repeat.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/back_repeat.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/back_repeat.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/discard-untrimmed.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/discard.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/dos.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/empty.fastq: empty data/atropos-1.1.24+dfsg/tests/cut/example.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/examplefront.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/highq.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/illumina.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/illumina.info.txt: Apache Hadoop Sequence file version 58 data/atropos-1.1.24+dfsg/tests/cut/illumina5.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/illumina5.info.txt: Apache Hadoop Sequence file version 58 data/atropos-1.1.24+dfsg/tests/cut/illumina64.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/insert.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/insert.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/interleaved.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/issue46.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/issue68.1.fq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/issue68.2.fq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/linked.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/lowercase.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/lowq.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/lowqual.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/maxlen.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/maxn0.2.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/maxn0.4.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/maxn0.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/maxn1.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/maxn2.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/minlen.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/minlen.noprimer.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/nextseq.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/no-trim.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/no_indels.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/overlapa.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/overlapb.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-filterboth.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-filterboth.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-filterboth_adapter.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-filterboth_adapter.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-filterboth_insert.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-filterboth_insert.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-m27.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-m27.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-onlyA.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-onlyA.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-separate.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-separate.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-too-short.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-too-short.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-trimmed.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-trimmed.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-untrimmed.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired-untrimmed.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired.m14.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired.m14.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_adapter.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_adapter.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_bis1_adapter.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_bis1_adapter.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_bis1_insert.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_bis1_insert.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_bis2_adapter.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_bis2_adapter.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_bis2_insert.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_bis2_insert.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_insert.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/paired_insert.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/pairedq.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/pairedq.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/pairedu.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/pairedu.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/plus.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/polya.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/rest.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/restfront.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/s_1_sequence.txt: ASCII text data/atropos-1.1.24+dfsg/tests/cut/small.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/small.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/small.trimmed.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/small.untrimmed.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/small_mincut1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/small_mincut2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/small_mincut3.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solid-no-zerocap.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solid.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solid.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solid5p-anchored.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solid5p-anchored.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solid5p-anchored.notrim.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solid5p-anchored.notrim.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solid5p.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solid5p.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solidbfast.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solidmaq.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/solidqual.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/sra.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/stripped.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/suffix.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/trimN3.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/trimN5.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/twoadapters.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/twoadapters.first.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/twoadapters.second.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/twoadapters.unknown.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/cut/unconditional-back.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/unconditional-both.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/unconditional-front.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/cut/wildcard.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/wildcardN.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/wildcard_adapter.fa: ASCII text data/atropos-1.1.24+dfsg/tests/cut/wildcard_adapter_anywhere.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/454.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/E3M.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/E3M.qual: ASCII text data/atropos-1.1.24+dfsg/tests/data/adapter.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/anchored-back.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/anchored.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/anchored_no_indels.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/anywhere_repeat.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/back_repeat.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/back_repeat.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/bad_bases.fq: ASCII text data/atropos-1.1.24+dfsg/tests/data/big.1.fq: ASCII text data/atropos-1.1.24+dfsg/tests/data/big.2.fq: ASCII text data/atropos-1.1.24+dfsg/tests/data/dos.fastq: ASCII text, with CRLF line terminators data/atropos-1.1.24+dfsg/tests/data/empty.fastq: empty data/atropos-1.1.24+dfsg/tests/data/example.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/highq.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/illumina.fastq.gz: gzip compressed data, last modified: Tue Mar 11 09:18:55 2014, from Unix, original size modulo 2^32 24252 data/atropos-1.1.24+dfsg/tests/data/illumina5.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/illumina64.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/insert.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/insert.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/interleaved.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/issue46.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/issue68.1.fq: ASCII text data/atropos-1.1.24+dfsg/tests/data/issue68.2.fq: ASCII text data/atropos-1.1.24+dfsg/tests/data/lengths.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/linked.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/lowq.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/lowqual.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/maxn.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/multiblock.fastq.gz: gzip compressed data, last modified: Wed Jul 27 11:44:02 2011, from Unix, original size modulo 2^32 184 data/atropos-1.1.24+dfsg/tests/data/nextseq.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/no_indels.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/overlapa.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/overlapb.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/paired.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/paired.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/paired_bis_adapter.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/paired_bis_adapter.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/paired_bis_insert.1.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/paired_bis_insert.2.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/plus.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/polya.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/prefix-adapter.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/rest.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/rest.txt: ASCII text data/atropos-1.1.24+dfsg/tests/data/restfront.txt: ASCII text data/atropos-1.1.24+dfsg/tests/data/s_1_sequence.txt.gz: gzip compressed data, was "compressed.fastq", last modified: Wed Mar 16 10:12:43 2011, from Unix, original size modulo 2^32 77 data/atropos-1.1.24+dfsg/tests/data/simple.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/simple.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/small.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/small.fastq.bz2: bzip2 compressed data, block size = 900k data/atropos-1.1.24+dfsg/tests/data/small.fastq.gz: gzip compressed data, was "small.fastq", last modified: Wed Jun 6 20:26:56 2012, from Unix, original size modulo 2^32 275 data/atropos-1.1.24+dfsg/tests/data/small.fastq.xz: XZ compressed data data/atropos-1.1.24+dfsg/tests/data/small.myownextension: ASCII text data/atropos-1.1.24+dfsg/tests/data/solid.csfasta: ASCII text, with very long lines data/atropos-1.1.24+dfsg/tests/data/solid.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/solid.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/solid.qual: ASCII text, with very long lines data/atropos-1.1.24+dfsg/tests/data/solid5p.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/solid5p.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/sra.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/data/suffix-adapter.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/toolong.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/tooshort.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/tooshort.noprimer.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/trimN3.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/trimN5.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/twoadapters.fasta: ASCII text data/atropos-1.1.24+dfsg/tests/data/wildcard.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/wildcardN.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/wildcard_adapter.fa: ASCII text data/atropos-1.1.24+dfsg/tests/data/withplus.fastq: ASCII text data/atropos-1.1.24+dfsg/tests/test_adapters.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_align.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_atropos.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_colorspace.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_commands.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_filters.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_modifiers.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_multicore.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_paired.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_qualtrim.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_seqio.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_trim.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/test_xopen.py: Python script text executable Python script, ASCII text executable data/atropos-1.1.24+dfsg/tests/utils.py: Python script, ASCII text executable data/atropos-1.1.24+dfsg/versioneer.py: ASCII text data/atropos-1.1.24+dfsg/debian/atropos.1: troff or preprocessor input, ASCII text data/atropos-1.1.24+dfsg/debian/changelog: ASCII text data/atropos-1.1.24+dfsg/debian/control: ASCII text data/atropos-1.1.24+dfsg/debian/copyright: ASCII text data/atropos-1.1.24+dfsg/debian/createmanpages: POSIX shell script, ASCII text executable data/atropos-1.1.24+dfsg/debian/manpages: ASCII text data/atropos-1.1.24+dfsg/debian/rules: a /usr/bin/make -f script, ASCII text executable data/atropos-1.1.24+dfsg/debian/source/format: ASCII text data/atropos-1.1.24+dfsg/debian/upstream/metadata: ASCII text data/atropos-1.1.24+dfsg/debian/watch: ASCII text data/atropos-1.1.24+dfsg/.pc/.version: ASCII text data/atropos-1.1.24+dfsg/.pc/.quilt_patches: ASCII text data/atropos-1.1.24+dfsg/.pc/.quilt_series: ASCII text data/atropos-1.1.24+dfsg/.pc/applied-patches: empty