This directory contains test files for testing various file formats supported by the boom package.

• test.fastq - Sample FASTQ file with 3 sequences
• test.fastq.gz - Gzip-compressed version of test.fastq
• test.fasta - Sample FASTA file with 3 sequences
• test.fasta.gz - Gzip-compressed version of test.fasta

• test.sam - Sample SAM alignment file
• test.bam - Sample BAM alignment file
• test-sort.bam - Sample sorted BAM alignment file (used for testing indexed access)
• test-sort.bam.bai - BAM index file for test-sort.bam

• test.vcf - Sample VCF (Variant Call Format) file with 5 variants across 2 chromosomes

FASTQ files contain sequence data with quality scores. Each record has 4 lines:

1. Sequence identifier (starts with @)
2. Nucleotide sequence
3. Plus sign (+)
4. Quality scores (same length as sequence)

FASTA files contain sequence data without quality scores. Each record has:

1. Sequence identifier line (starts with >)
2. One or more lines of sequence data

SAM (Sequence Alignment/Map) and BAM (binary SAM) files contain aligned sequence data:

• SAM is a text-based format
• BAM is a compressed binary format
• BAI files are index files for BAM files enabling rapid random access

VCF (Variant Call Format) files contain variant call data:

• VCF is a text-based format for storing gene sequence variations
• Each record represents a genomic variant with position, reference, and alternate alleles
• Can include sample genotype information and quality metrics

These test files are used by the tests to verify that:

• FASTQ files can be opened and handled (fastq_fasta_test.go)
• FASTA files can be opened and handled (fastq_fasta_test.go)
• SAM/BAM alignment files can be opened and handled (sam_bam_test.go)
• VCF variant files can be opened and handled (vcf_test.go)
• BAM index files can be loaded and used for random access (index_test.go)
• Compressed versions (gzip) of various formats can be handled
• The htslib wrapper correctly interfaces with these file formats

Example programs in the examples/ directory also use these test files.