├── .github └── workflows │ └── upload.yaml ├── .gitignore ├── CONTRIBUTING.md ├── LICENSE ├── Makefile ├── README.md ├── data ├── README.md ├── bam │ ├── bad │ │ ├── bai_older_than_data.bam │ │ ├── bai_older_than_data.bam.bai │ │ ├── read_name_longer_than_254.sam │ │ └── truncated.bam │ └── good │ │ ├── basic.bam │ │ ├── basic.sam │ │ ├── basic_unsorted.bam │ │ ├── compressed.sam.gz │ │ ├── indexed_bai.bam │ │ ├── indexed_bai.bam.bai │ │ ├── indexed_csi.bam │ │ ├── indexed_csi.bam.csi │ │ ├── indexed_csi.sam.gz │ │ ├── indexed_csi.sam.gz.csi │ │ ├── indexed_tbi.sam.gz │ │ ├── indexed_tbi.sam.gz.tbi │ │ └── no_mapped_reads.bam ├── bed │ ├── bad │ │ ├── negative_coords.bed │ │ ├── non_integer_coords.bed │ │ ├── spaces.bed │ │ └── start_greater_than_end_coords.bed │ └── good │ │ ├── basic.bed │ │ ├── compressed.bed.gz │ │ ├── indexed_csi.bed.gz │ │ ├── indexed_csi.bed.gz.csi │ │ ├── indexed_tbi.bed.gz │ │ ├── indexed_tbi.bed.gz.tbi │ │ └── unsorted.bed ├── fasta │ └── good │ │ ├── basic_aligned.fa │ │ ├── basic_dna.fa │ │ ├── basic_protein.fa │ │ ├── compressed.fa.gz │ │ ├── duplicate_sequence_names.fa │ │ ├── empty_lines.fa │ │ ├── multiline.fa │ │ └── name_contains_spaces.fa ├── fastq │ ├── bad │ │ ├── quality_mismatch.fastq │ │ ├── truncated_clean.fastq │ │ └── truncated_halfway.fastq │ └── good │ │ ├── basic_R1.fastq │ │ ├── basic_R2.fastq │ │ ├── compressed.fastq.gz │ │ ├── duplicate_+.fastq │ │ ├── interleaved.fastq │ │ ├── multiline.fastq │ │ └── quality_@.fastq └── vcf │ ├── bad │ └── missing_info_field.vcf │ └── good │ ├── basic.bcf │ ├── basic.vcf │ ├── basic_multisample.bcf │ ├── basic_multisample.vcf │ ├── compressed.vcf.gz │ ├── indexed.bcf │ ├── indexed.bcf.csi │ ├── indexed_csi.vcf.gz │ ├── indexed_csi.vcf.gz.csi │ ├── indexed_tbi.vcf.gz │ └── indexed_tbi.vcf.gz.tbi ├── metadata.csv └── src ├── generate_bam.sh ├── generate_bed.sh ├── generate_fasta.sh ├── generate_fastq.sh ├── generate_vcf.sh └── lib.sh /.github/workflows/upload.yaml: 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