├── .gitignore ├── Cargo.toml ├── LICENSE ├── README.md ├── rustfmt.toml ├── src ├── annotation.rs ├── bam.rs ├── convert.rs ├── lib.rs ├── main.rs ├── position.rs ├── query_bam_records.rs └── rad.rs └── tests ├── NC_002333.2.fna ├── NC_002333.2.gff ├── NC_002333.2.gtf ├── NC_002333.2.sam ├── NC_007112.7_1525.gtf ├── NC_007112.7_1525.sam ├── NC_007112.7_1631.gtf ├── NC_007112.7_1631.sam ├── NC_007112.7_2017.gtf ├── NC_007112.7_2017.sam ├── NC_007114.7_12427.gtf ├── NC_007114.7_12427.sam ├── NC_007120.7_12427.gtf ├── NC_007120.7_12427.sam ├── NC_007131.7_6185.gtf ├── NC_007131.7_6185.sam ├── annotations_test.rs ├── bam_test.rs ├── gencode_v35_index ├── gtf.exon ├── gtf.len ├── gtf.map └── gtf.name ├── missing_mate.sam ├── missing_mate2.sam ├── missing_mate3.sam ├── multi_exons.sam ├── not_name_sorted.sam ├── overhang_cigar_test.rs ├── paired.sam ├── query_bam_records_test.rs ├── single_exon.sam └── single_exon2.sam /.gitignore: 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