├── .gitattributes ├── README.md ├── data ├── align.sh ├── blastn.sh ├── bwa.sh ├── mafft.sh ├── out.blastn.m6 ├── out.blastn.toself.m6 ├── out.bwa.bam ├── out.bwa.bam.bai ├── out.mafft.msa ├── out.sam ├── read.se.fa ├── read.se.fa.nhr ├── read.se.fa.nin ├── read.se.fa.nsq ├── ref.fa ├── ref.fa.amb ├── ref.fa.ann ├── ref.fa.bwt ├── ref.fa.nhr ├── ref.fa.nin ├── ref.fa.nsq ├── ref.fa.pac ├── ref.fa.sa ├── ref.read.fa ├── ref.read.fa.mafft.reformated.msa.save └── tmp ├── git.rm.sh ├── git.sh ├── src ├── bam2msa ├── bam2msa.cr ├── bam2msa_final.wasm ├── cr.to.wasm.sh ├── lib │ └── admiral │ │ ├── .travis.yml │ │ ├── CONTRIBUTING.md │ │ ├── LICENSE │ │ ├── Makefile │ │ ├── README.md │ │ ├── docs │ │ ├── Admiral.html │ │ ├── Admiral │ │ │ ├── ArgumentList.html │ │ │ ├── Command.html │ │ │ ├── Command │ │ │ │ └── MissingArgument.html │ │ │ ├── Error.html │ │ │ └── StringValue.html │ │ ├── Array.html │ │ ├── Set.html │ │ ├── css │ │ │ └── style.css │ │ ├── index.html │ │ ├── index.json │ │ ├── js │ │ │ └── doc.js │ │ └── search-index.js │ │ ├── examples │ │ ├── basic.cr │ │ ├── complex.cr │ │ └── hello.cr │ │ ├── shard.yml │ │ ├── spec │ │ ├── admiral │ │ │ ├── flag_spec.cr │ │ │ └── rescue_from_spec.cr │ │ └── fixtures │ │ │ ├── basic.cr │ │ │ ├── basic_with_default.cr │ │ │ ├── required_typed.cr │ │ │ ├── rescue_from.cr │ │ │ ├── typed.cr │ │ │ └── typed_with_default.cr │ │ └── src │ │ ├── admiral.cr │ │ ├── admiral │ │ ├── argument_list.cr │ │ ├── command.cr │ │ ├── command │ │ │ ├── argument.cr │ │ │ ├── flag.cr │ │ │ ├── help.cr │ │ │ ├── rescue.cr │ │ │ ├── runner.cr │ │ │ ├── sub_command.cr │ │ │ └── version.cr │ │ ├── error.cr │ │ └── string_value.cr │ │ └── core_ext │ │ └── types.cr └── readfasta.cr └── test ├── bam2msa ├── bam2msa.cr ├── bam2msa_demo3.png ├── case ├── control ├── demo.sh ├── lib ├── out.bam2msa ├── out.bam2msa.msa ├── out.bwa.bam ├── out.bwa.bam.bai ├── out.sam ├── read.se.fa ├── readfasta.cr └── ref.fa /.gitattributes: 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