├── .gitignore ├── .travis.yml ├── Cargo.lock ├── Cargo.toml ├── LICENSE ├── README.md ├── ci ├── before_deploy.sh ├── construct_linux_binary.py ├── install.sh ├── script.sh ├── sha256.sh └── utils.sh ├── editdistancealleles.py ├── paper ├── AML_508084.txt ├── AML_548327.txt ├── AML_721214.txt ├── AML_782328.txt ├── AML_809653.txt ├── coverage.png ├── figure2.R ├── figure3.R ├── figureS2.R ├── figures │ ├── figure2-updated.pdf │ ├── figure3-newlayout.pdf │ ├── figureS1.pdf │ ├── figureS2.pdf │ └── workflow-updated.pdf ├── main.tex ├── sample_gt.txt ├── schlacount.bib ├── table1_AML_DRB1.tsv ├── table2_AML_C.tsv ├── table4_paulson_discovery.R └── workflow.png ├── prepare_reference.sh ├── src ├── config.rs ├── em.rs ├── hla.rs ├── io.rs ├── locus.rs ├── main.rs └── mapping.rs └── test ├── barcodes0.tsv ├── barcodes1.tsv ├── barcodes7.tsv ├── cds_ABC.fa ├── fake_db ├── Allele_status.txt ├── hla_gen.fasta ├── hla_nuc.fasta └── hla_nuc.fasta.idx ├── genomic_ABC.fa ├── test.bam ├── 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