├── .github └── workflows │ ├── c-cpp.yml │ ├── docker.yml │ ├── macosx.yml │ ├── npm-install.yml │ └── release.yml ├── .gitignore ├── .gitmodules ├── AUTHORS ├── CONTRIBUTING.md ├── CREDITS ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── alfred.png ├── client ├── .gitignore ├── package-lock.json ├── package.json └── src │ ├── index.html │ └── static │ ├── css │ ├── alfred.css │ └── gear.css │ ├── examples │ ├── atac.illumina.pe.ms.json.gz │ ├── chip.illumina.se.ms.json.gz │ ├── dna.exome.illumina.pe.ms.json.gz │ ├── dna.wgs.illumina.mp.ms.json.gz │ ├── dna.wgs.illumina.pe.ms.json.gz │ ├── dna.wgs.ont.se.ms.json.gz │ ├── dna.wgs.pacbio.se.ms.json.gz │ ├── examples.json │ ├── hic.illumina.pe.ms.json.gz │ ├── rna.illumina.pe.ms.json.gz │ └── tenX.illumina.pe.json.gz │ ├── img │ ├── embl.svg │ └── pattern.png │ └── js │ └── alfred.js ├── docs ├── .gitignore ├── .vuepress │ ├── .gitignore │ └── config.js ├── README.md ├── cli │ └── README.md ├── faq │ └── README.md ├── images │ └── alfred.png ├── installation │ └── README.md ├── package-lock.json ├── package.json └── webapp │ └── README.md ├── example ├── E.coli.cram ├── E.coli.cram.crai ├── E.coli.fa.gz ├── E.coli.fa.gz.fai ├── E.coli.fa.gz.gzi ├── example.sh └── split_ase_example.sh ├── gtf └── downloadGTF.sh ├── maps ├── exon.R └── promoter.R ├── motif ├── downloadMotifs.sh ├── jaspar.nonredundant.gz └── rss.gz ├── scripts ├── gc.R ├── merge.py ├── rd.R ├── reppattern.R ├── reptime.R └── stats.R ├── singularity ├── README.md └── alfred.def ├── src ├── alfred.cpp ├── align.h ├── annotate.h ├── ase.h ├── bam2match.h ├── bamstats.h ├── barcode.h ├── bcsplit.h ├── bed.h ├── consedlib.h ├── consensus.h ├── count_dna.h ├── count_junction.h ├── count_rna.h ├── edlib.cpp ├── edlib.h ├── gff3.h ├── gotoh.h ├── gtf.h ├── jlib │ └── nlohmann │ │ └── json.hpp ├── json.h ├── motif.h ├── msa.h ├── needle.h ├── pwalign.h ├── pwedit.h ├── qc.h ├── qcstruct.h ├── repliseq.h ├── repliseqproc.h ├── spaced.h ├── split.h ├── 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