├── .github ├── dependabot.yml └── workflows │ ├── conventional-prs.yml │ ├── release-please.yml │ └── rust.yml ├── .gitignore ├── .gitmodules ├── CHANGELOG.md ├── Cargo.toml ├── LICENSE.md ├── README.md ├── config.toml ├── src ├── bam │ ├── buffer.rs │ ├── ext.rs │ ├── header.rs │ ├── index.rs │ ├── mod.rs │ ├── pileup.rs │ ├── record.rs │ └── record_serde.rs ├── bcf │ ├── buffer.rs │ ├── header.rs │ ├── index.rs │ ├── mod.rs │ └── record.rs ├── bgzf │ └── mod.rs ├── errors.rs ├── faidx │ └── mod.rs ├── htslib.rs ├── lib.rs ├── tbx │ └── mod.rs ├── tpool.rs └── utils.rs └── test ├── bam2sam_expected.sam ├── bam2sam_out.sam ├── bam2sam_test.bam ├── base_mods ├── MM-double.sam └── MM-orient.sam ├── bgzip ├── bgzip.vcf.gz ├── gzip.vcf.gz └── plain.vcf ├── obs-cornercase.vcf ├── results └── .gitignore ├── tabix_reader ├── bad_header.txt.gz ├── bad_header.txt.gz.tbi ├── genomic_positions_header.txt.gz ├── genomic_positions_header.txt.gz.tbi ├── genomic_regions_header.txt.gz ├── genomic_regions_header.txt.gz.tbi ├── test_bed3.bed.gz └── test_bed3.bed.gz.tbi ├── test-info-multi-string-number=A.vcf ├── test-info-multi-string.vcf ├── test.bam ├── test.bam.bai ├── test.bcf ├── test.bcf.csi ├── test_cram.bam ├── test_cram.bam.bai ├── test_cram.cram ├── test_cram.cram.crai ├── test_cram.fa ├── test_cram.fa.fai ├── test_cram.sam ├── test_different_index_name.bam ├── test_headers.out.vcf ├── test_headers.vcf ├── test_index_build.bam ├── test_issue_156_no_text.bam ├── test_left.vcf ├── test_left.vcf.gz ├── test_left.vcf.gz.tbi ├── test_missing.vcf ├── test_multi.bcf ├── test_non_diploid.vcf ├── test_nonstandard_orientation.sam ├── test_orientation_supplementary.sam ├── test_paired.sam ├── test_right.vcf ├── test_right.vcf.gz ├── test_right.vcf.gz.tbi ├── test_spliced_reads.bam ├── test_spliced_reads.bam.bai ├── test_string.vcf ├── test_svlen.vcf ├── test_trailing_omitted_format.vcf ├── test_unmapped.bam ├── test_unmapped.bam.bai ├── test_unmapped.cram ├── 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