CONTRIBUTING.rst
MANIFEST.in
README.rst
requirements.txt
requirements_dev.txt
requirements_tools.txt
requirements_tools_linux_only.txt
setup.cfg
setup.py
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/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/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/ERR.fastq
bioconvert/data/ERR3295124.fastq
bioconvert/data/JB409847.embl
bioconvert/data/JB409847.ena
bioconvert/data/README.rst
bioconvert/data/SRR390728_1.fastq
bioconvert/data/SRR390728_1.fastq.gz
bioconvert/data/SRR390728_2.fastq
bioconvert/data/SRR390728_2.fastq.gz
bioconvert/data/SRR6477205.fastq
bioconvert/data/SRR6477205.fastq.gz
bioconvert/data/SRR8954470_1.fastq
bioconvert/data/SRR8954470_2.fastq
bioconvert/data/__init__.py
bioconvert/data/biocode.gb
bioconvert/data/biocode.gff
bioconvert/data/biopython.clustal
bioconvert/data/biopython.fasta
bioconvert/data/biopython.newick
bioconvert/data/biopython.nexus
bioconvert/data/biopython.phylip
bioconvert/data/biopython.stockholm
bioconvert/data/exp_SP1.fq
bioconvert/data/goalign.clustal
bioconvert/data/goalign.fasta
bioconvert/data/goalign.nexus
bioconvert/data/goalign.phylip
bioconvert/data/gotree.newick
bioconvert/data/gotree.nexus
bioconvert/data/gotree.xml
bioconvert/data/hg38.chrom.sizes
bioconvert/data/measles.chrom.sizes
bioconvert/data/measles.fa
bioconvert/data/measles.fa.amb
bioconvert/data/measles.fa.ann
bioconvert/data/measles.fa.bwt
bioconvert/data/measles.fa.fai
bioconvert/data/measles.fa.pac
bioconvert/data/measles.fa.sa
bioconvert/data/measles_R1.fastq.gz
bioconvert/data/measles_R2.fastq.gz
bioconvert/data/nexus2clustal_biopython.clustal
bioconvert/data/nexus2clustal_biopython.nexus
bioconvert/data/nexus2clustal_squizz.clustal
bioconvert/data/nexus2clustal_squizz.nexus
bioconvert/data/nexus2fasta_biopython.fasta
bioconvert/data/nexus2fasta_biopython.nexus
bioconvert/data/nexus2fasta_goalign.nexus
bioconvert/data/nexus2fasta_squizz.fasta
bioconvert/data/nexus2fasta_squizz.nexus
bioconvert/data/plink_toy.bed
bioconvert/data/plink_toy.bim
bioconvert/data/plink_toy.fam
bioconvert/data/plink_toy.map
bioconvert/data/plink_toy.ped
bioconvert/data/plink_toy.vcf
bioconvert/data/sample_v2.fasta
bioconvert/data/sample_v2.fastq
bioconvert/data/sample_v2.fastq.gz
bioconvert/data/sample_v2.scf
bioconvert/data/sample_v3.fasta
bioconvert/data/sample_v3.fastq
bioconvert/data/sample_v3.fastq.gz
bioconvert/data/sample_v3.scf
bioconvert/data/sample_v4.fasta
bioconvert/data/sample_v4.fastq
bioconvert/data/sample_v4.fastq.gz
bioconvert/data/squizz.clustal
bioconvert/data/squizz.fasta
bioconvert/data/squizz.phylip
bioconvert/data/squizz.stockholm
bioconvert/data/test_SP1.fq.dsrc
bioconvert/data/test_SP1.fq.gz
bioconvert/data/test_bam2wiggle.wiggle
bioconvert/data/test_bcf2vcf_v1.bcf
bioconvert/data/test_bcf2wiggle.wiggle
bioconvert/data/test_bedgraph2bed.bedgraph
bioconvert/data/test_bedgraph2wiggle.wiggle
bioconvert/data/test_bigwig2wiggle.wiggle
bioconvert/data/test_example1.asqg
bioconvert/data/test_fasta2faa.faa
bioconvert/data/test_fasta2faa.fasta
bioconvert/data/test_fasta2faa_ali.faa
bioconvert/data/test_fasta2fastq.fastq
bioconvert/data/test_fasta2fastq.qual
bioconvert/data/test_fastq2fasta_v1.fasta
bioconvert/data/test_fastq2fasta_v1.fastq
bioconvert/data/test_fastq2fasta_v1.fastq.gz
bioconvert/data/test_genbank.gbk
bioconvert/data/test_gfa2fasta.fasta
bioconvert/data/test_gfa2fasta.gfa
bioconvert/data/test_gfa2fasta_v1.gfa
bioconvert/data/test_maf2sam.maf
bioconvert/data/test_maf2sam.sam
bioconvert/data/test_measles.bam
bioconvert/data/test_measles.bed
bioconvert/data/test_measles.bed.gz
bioconvert/data/test_measles.bigwig
bioconvert/data/test_measles.cram
bioconvert/data/test_measles.fa
bioconvert/data/test_measles.fa.fai
bioconvert/data/test_measles.gbk
bioconvert/data/test_measles.sam
bioconvert/data/test_measles.sorted.bam
bioconvert/data/test_measles.sorted.bam.bai
bioconvert/data/test_measles.sorted.bigwig
bioconvert/data/test_measles.sorted.json
bioconvert/data/test_measles_unpaired.sorted.bam
bioconvert/data/test_measles_unpaired.sorted.bam.bai
bioconvert/data/test_measles_unpaired.sorted.cram
bioconvert/data/test_phylip2xmfa.xmfa
bioconvert/data/test_pybigwig.bed
bioconvert/data/test_pybigwig.bigbed
bioconvert/data/test_tabulated.csv
bioconvert/data/test_tabulated.ods
bioconvert/data/test_tabulated.tsv
bioconvert/data/test_tabulated.xls
bioconvert/data/test_tabulated.xlsx
bioconvert/data/test_tabulated_multi_page.0.csv
bioconvert/data/test_tabulated_multi_page.1.csv
bioconvert/data/test_tabulated_multi_page.xls
bioconvert/data/test_tabulated_with_3_more_blank_lines.csv
bioconvert/data/test_ucsc_bed2wiggle.wiggle
bioconvert/data/test_v1.json
bioconvert/data/test_v1.yaml
bioconvert/data/test_v1_nocomments.yaml
bioconvert/data/test_vcf2bcf_v1.bed
bioconvert/data/test_vcf2bcf_v1.vcf
bioconvert/data/test_vcf2bed_v1.bed
bioconvert/data/test_vcf2wiggle.wiggle
bioconvert/data/test_wig2bed.bed
bioconvert/data/test_wig2bed.wig
bioconvert/data/ucsc.2bit
bioconvert/data/ucsc.bed
bioconvert/data/ucsc.bedgraph
bioconvert/data/ucsc.bg
bioconvert/data/ucsc.bigbed
bioconvert/data/ucsc.bigwig
bioconvert/data/ucsc.fasta
bioconvert/data/ucsc.wiggle
bioconvert/data/testing/__init__.py
bioconvert/data/testing/genbank2fasta/__init__.py
bioconvert/data/testing/sam2paf/__init__.py
bioconvert/data/testing/sam2paf/create_files.sh
bioconvert/io/__init__.py
bioconvert/io/embl.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/io/sniffer.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/sniffer.py
bioconvert/scripts/stats.py
bioconvert/simulator/__init__.py
bioconvert/simulator/fasta.py
bioconvert/simulator/fastq.py
bioconvert/simulator/gfa.py
bioconvert/validator/__init__.py
bioconvert/validator/asqg_lint.py
bioconvert/validator/gfa_lint.py
bioconvert/validator/sam_lint.py
examples/README.txt
examples/conversion.png
examples/plot_benchmark.py
examples/plot_graph.py
examples/plot_methods.py