├── .github └── workflows │ └── ci.yml ├── CHANGELOG.md ├── Cargo.lock ├── Cargo.toml ├── LICENSE-THIRDPARTY.json ├── LICENSE.md ├── README.md ├── docs ├── methods.md └── user_guide.md ├── img └── portello_igv_example.png ├── lib └── rust-vc-utils │ ├── CHANGELOG.md │ ├── Cargo.toml │ ├── LICENSE.md │ ├── README.md │ ├── src │ ├── bam_utils │ │ ├── aux │ │ │ ├── mod.rs │ │ │ └── sa_tag_parser.rs │ │ ├── bam_reader_utils.rs │ │ ├── bam_record_utils.rs │ │ ├── basemod.rs │ │ ├── cigar │ │ │ ├── clip_alignment.rs │ │ │ ├── mod.rs │ │ │ ├── score_alignment.rs │ │ │ └── shift_indels │ │ │ │ ├── cigar_indel_shifter.rs │ │ │ │ ├── left_shift_indels.rs │ │ │ │ ├── mod.rs │ │ │ │ └── right_shift_indels.rs │ │ ├── mod.rs │ │ ├── read_to_ref_map.rs │ │ ├── split_read.rs │ │ └── util.rs │ ├── bigwig_utils.rs │ ├── chrom_list.rs │ ├── containers.rs │ ├── genome_ref.rs │ ├── genome_segment.rs │ ├── indel_breakend_homology.rs │ ├── int_range.rs │ ├── lib.rs │ ├── prob_util.rs │ ├── 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