.coveragerc
.dockerignore
.gitignore
.readthedocs.yml
CONTRIBUTING.rst
COPYING
COPYRIGHT
Dockerfile
MANIFEST.in
README.rst
conversion.dot
environment.yml
environment_rtd.yml
requirements.txt
requirements_dev.txt
setup.cfg
setup.py
.github/issue_template.md
.github/workflows/abi2fasta.yml
.github/workflows/abi2fastq.yml
.github/workflows/abi2qual.yml
.github/workflows/bam2bedgraph.yml
.github/workflows/bam2bigwig.yml
.github/workflows/bam2cov.yml
.github/workflows/bam2cram.yml
.github/workflows/bam2fasta.yml
.github/workflows/bam2fastq.yml
.github/workflows/bam2json.yml
.github/workflows/bam2sam.yml
.github/workflows/bam2tsv.yml
.github/workflows/bam2wiggle.yml
.github/workflows/bcf2vcf.yml
.github/workflows/bcf2wiggle.yml
.github/workflows/bed2wiggle.yml
.github/workflows/bedgraph2bigwig.yml
.github/workflows/bedgraph2cov.yml
.github/workflows/bedgraph2wiggle.yml
.github/workflows/bigbed2bed.yml
.github/workflows/bigbed2wiggle.yml
.github/workflows/bigwig2bedgraph.yml
.github/workflows/bigwig2wiggle.yml
.github/workflows/bplink2plink.yml
.github/workflows/bplink2vcf.yml
.github/workflows/bz22gz.yml
.github/workflows/clustal2fasta.yml
.github/workflows/clustal2nexus.yml
.github/workflows/clustal2phylip.yml
.github/workflows/clustal2stockholm.yml
.github/workflows/core.yml
.github/workflows/cram2bam.yml
.github/workflows/cram2fasta.yml
.github/workflows/cram2fastq.yml
.github/workflows/cram2sam.yml
.github/workflows/csv2tsv.yml
.github/workflows/csv2xls.yml
.github/workflows/dsrc2gz.yml
.github/workflows/embl2fasta.yml
.github/workflows/embl2genbank.yml
.github/workflows/fasta2clustal.yml
.github/workflows/fasta2faa.yml
.github/workflows/fasta2fasta_agp.yml
.github/workflows/fasta2fastq.yml
.github/workflows/fasta2genbank.yml
.github/workflows/fasta2nexus.yml
.github/workflows/fasta2phylip.yml
.github/workflows/fasta2twobit.yml
.github/workflows/fasta_qual2fastq.yml
.github/workflows/fastq2fasta.yml
.github/workflows/fastq2fasta_qual.yml
.github/workflows/fastq2qual.yml
.github/workflows/genbank2embl.yml
.github/workflows/genbank2fasta.yml
.github/workflows/genbank2gff3.yml
.github/workflows/gfa2fasta.yml
.github/workflows/gff22gff3.yml
.github/workflows/gff32gff2.yml
.github/workflows/gz2bz2.yml
.github/workflows/gz2dsrc.yml
.github/workflows/json2yaml.yml
.github/workflows/maf2sam.yml
.github/workflows/main.yml
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.github/workflows/newick2phyloxml.yml
.github/workflows/nexus2clustal.yml
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.github/workflows/nexus2newick.yml
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.github/workflows/ods2csv.yml
.github/workflows/phylip2clustal.yml
.github/workflows/phylip2fasta.yml
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.github/workflows/phylip2xmfa.yml
.github/workflows/phyloxml2newick.yml
.github/workflows/phyloxml2nexus.yml
.github/workflows/plink2bplink.yml
.github/workflows/plink2vcf.yml
.github/workflows/pypi.yml
.github/workflows/sam2bam.yml
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.github/workflows/sam2paf.yml
.github/workflows/scf2fasta.yml
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.github/workflows/stockholm2clustal.yml
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.github/workflows/tsv2csv.yml
.github/workflows/twobit2fasta.yml
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.github/workflows/vcf2bplink.yml
.github/workflows/vcf2plink.yml
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.github/workflows/xls2csv.yml
.github/workflows/xlsx2csv.yml
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.github/workflows/yaml2json.yml
Singularity/Singularity
Singularity/Singularity.0_1_0
Singularity/Singularity.0_1_3
Singularity/Singularity.0_2_0
Singularity/Singularity.0_3_0
Singularity/Singularity.0_4_2
Singularity/Singularity.0_5_0
bioconvert/__init__.py
bioconvert/abi2fasta.py
bioconvert/abi2fastq.py
bioconvert/abi2qual.py
bioconvert/bam2bedgraph.py
bioconvert/bam2bigwig.py
bioconvert/bam2cov.py
bioconvert/bam2cram.py
bioconvert/bam2fasta.py
bioconvert/bam2fastq.py
bioconvert/bam2json.py
bioconvert/bam2sam.py
bioconvert/bam2tsv.py
bioconvert/bam2wiggle.py
bioconvert/bcf2vcf.py
bioconvert/bcf2wiggle.py
bioconvert/bed2wiggle.py
bioconvert/bedgraph2bigwig.py
bioconvert/bedgraph2cov.py
bioconvert/bedgraph2wiggle.py
bioconvert/bigbed2bed.py
bioconvert/bigbed2wiggle.py
bioconvert/bigwig2bedgraph.py
bioconvert/bigwig2wiggle.py
bioconvert/bplink2plink.py
bioconvert/bplink2vcf.py
bioconvert/bz22gz.py
bioconvert/clustal2fasta.py
bioconvert/clustal2nexus.py
bioconvert/clustal2phylip.py
bioconvert/clustal2stockholm.py
bioconvert/cram2bam.py
bioconvert/cram2fasta.py
bioconvert/cram2fastq.py
bioconvert/cram2sam.py
bioconvert/csv2tsv.py
bioconvert/csv2xls.py
bioconvert/dsrc2gz.py
bioconvert/embl2fasta.py
bioconvert/embl2genbank.py
bioconvert/fasta2clustal.py
bioconvert/fasta2faa.py
bioconvert/fasta2fasta_agp.py
bioconvert/fasta2fastq.py
bioconvert/fasta2genbank.py
bioconvert/fasta2nexus.py
bioconvert/fasta2phylip.py
bioconvert/fasta2twobit.py
bioconvert/fasta_qual2fastq.py
bioconvert/fastq2fasta.py
bioconvert/fastq2fasta_qual.py
bioconvert/fastq2qual.py
bioconvert/genbank2embl.py
bioconvert/genbank2fasta.py
bioconvert/genbank2gff3.py
bioconvert/gfa2fasta.py
bioconvert/gff22gff3.py
bioconvert/gff2genbank.py
bioconvert/gff32gff2.py
bioconvert/gz2bz2.py
bioconvert/gz2dsrc.py
bioconvert/json2yaml.py
bioconvert/maf2sam.py
bioconvert/newick2nexus.py
bioconvert/newick2phyloxml.py
bioconvert/nexus2clustal.py
bioconvert/nexus2fasta.py
bioconvert/nexus2newick.py
bioconvert/nexus2phylip.py
bioconvert/nexus2phyloxml.py
bioconvert/ods2csv.py
bioconvert/phylip2clustal.py
bioconvert/phylip2fasta.py
bioconvert/phylip2nexus.py
bioconvert/phylip2stockholm.py
bioconvert/phylip2xmfa.py
bioconvert/phyloxml2newick.py
bioconvert/phyloxml2nexus.py
bioconvert/plink2bplink.py
bioconvert/plink2vcf.py
bioconvert/sam2bam.py
bioconvert/sam2cram.py
bioconvert/sam2paf.py
bioconvert/scf2fasta.py
bioconvert/scf2fastq.py
bioconvert/sra2fastq.py
bioconvert/stockholm2clustal.py
bioconvert/stockholm2phylip.py
bioconvert/tsv2csv.py
bioconvert/twobit2fasta.py
bioconvert/vcf2bcf.py
bioconvert/vcf2bed.py
bioconvert/vcf2bplink.py
bioconvert/vcf2plink.py
bioconvert/vcf2wiggle.py
bioconvert/wig2bed.py
bioconvert/xls2csv.py
bioconvert/xlsx2csv.py
bioconvert/xmfa2phylip.py
bioconvert/yaml2json.py
bioconvert.egg-info/PKG-INFO
bioconvert.egg-info/SOURCES.txt
bioconvert.egg-info/dependency_links.txt
bioconvert.egg-info/entry_points.txt
bioconvert.egg-info/not-zip-safe
bioconvert.egg-info/requires.txt
bioconvert.egg-info/top_level.txt
bioconvert/core/__init__.py
bioconvert/core/base.py
bioconvert/core/benchmark.py
bioconvert/core/converter.py
bioconvert/core/decorators.py
bioconvert/core/downloader.py
bioconvert/core/extensions.py
bioconvert/core/graph.py
bioconvert/core/init.py
bioconvert/core/levenshtein.py
bioconvert/core/registry.py
bioconvert/core/shell.py
bioconvert/core/utils.py
bioconvert/data/README.rst
bioconvert/data/__init__.py
bioconvert/data/measles.chrom.sizes
bioconvert/data/test.bigwig
bioconvert/data/test_SP1.fq.gz
bioconvert/data/test_gfa2fasta_v1.gfa
bioconvert/data/test_measles.fa.fai
bioconvert/data/test_measles.sorted.bam
bioconvert/data/testing/__init__.py
bioconvert/data/testing/genbank2fasta/JB409847.gbk
bioconvert/data/testing/genbank2fasta/README.rst
bioconvert/data/testing/genbank2fasta/__init__.py
bioconvert/data/testing/sam2paf/Makefile
bioconvert/data/testing/sam2paf/README.rst
bioconvert/data/testing/sam2paf/__init__.py
bioconvert/data/testing/sam2paf/create_files.sh
bioconvert/data/testing/sam2paf/test_sam2paf_bad1.sam
bioconvert/data/testing/sam2paf/test_sam2paf_bad2.sam
bioconvert/data/testing/sam2paf/test_sam2paf_extra.sam
bioconvert/data/testing/sam2paf/test_sam2paf_v1.paf
bioconvert/data/testing/sam2paf/test_sam2paf_v1.sam
bioconvert/io/__init__.py
bioconvert/io/fasta.py
bioconvert/io/genbank.py
bioconvert/io/gff2.py
bioconvert/io/gff3.py
bioconvert/io/maf.py
bioconvert/io/scf.py
bioconvert/misc/README.rst
bioconvert/misc/__init__.py
bioconvert/misc/cython_fastq2fasta.pyx
bioconvert/misc/fastq2fasta.c
bioconvert/misc/fastq2fasta.pl
bioconvert/misc/install_goalign.sh
bioconvert/misc/install_gotree.sh
bioconvert/scripts/__init__.py
bioconvert/scripts/converter.py
bioconvert/scripts/init_convert.py
bioconvert/scripts/stats.py
bioconvert/simulator/__init__.py
bioconvert/simulator/fasta.py
bioconvert/simulator/fastq.py
bioconvert/simulator/gfa.py
bioconvert/utils/__init__.py
bioconvert/utils/biocode/README.rst
bioconvert/utils/biocode/__init__.py
bioconvert/utils/biocode/annotation.py
bioconvert/utils/biocode/convert_genbank_to_gff3.py
bioconvert/utils/biocode/gff.py
bioconvert/utils/biocode/tbl.py
bioconvert/utils/biocode/things.py
bioconvert/utils/biocode/utils.py
doc/CONTRIB.rst
doc/ChangeLog.rst
doc/Makefile
doc/Snakefile
doc/Snakefile_benchmark
doc/benchmark.png
doc/benchmark2.png
doc/benchmarking.rst
doc/bibliography.rst
doc/conf.py
doc/conversion.png
doc/conversion.svg
doc/coverage_igv.png
doc/create_automodules_allconverters.py
doc/create_graph.py
doc/developer_guide.rst
doc/faqs.rst
doc/formats.rst
doc/glossary.rst
doc/index.rst
doc/install_singularity.sh
doc/installation.rst
doc/multi_benchmark.png
doc/ref_converters.rst
doc/ref_core.rst
doc/ref_io.rst
doc/references.rst
doc/script.sh
doc/script2.sh
doc/stats.csv
doc/tutorial.rst
doc/user_guide.rst
doc/_static/NewickExample.svg
doc/_static/basic.css
doc/_static/benchmark_fastq2fasta.png
examples/README.txt
examples/conversion.dot
examples/conversion.png
examples/plot_benchmark.py
examples/plot_graph.py
examples/plot_methods.py
examples/test.cov