samtools bindings for Go

This package provides Go bindings for the htslib library, supporting:

• SAM/BAM files for sequence alignment data
• VCF/BCF files for variant call data

This package requires htslib to be installed on your system.

Ubuntu/Debian:

sudo apt-get install libhts-dev

Fedora/RHEL:

sudo dnf install htslib-devel

macOS:

brew install htslib

go get github.com/yassineS/boom

• Go 1.24 or later
• htslib 1.19 or later

See https://www.htslib.org/ for htslib documentation.

The package includes comprehensive tests for handling various file formats supported by htslib:

• SAM/BAM files (sam_bam_test.go) - Tests for reading and writing sequence alignment data
• VCF files (vcf_test.go) - Tests for reading variant call data
• FASTQ/FASTA files (fastq_fasta_test.go) - Tests for reading sequence data
• BAM indexing (index_test.go) - Tests for loading and using BAM index files for random access
• Compressed formats - Tests for handling gzip-compressed versions (.gz)

To run tests:

go test -v

Note: Tests require htslib to be installed. If htslib is not available, tests will be skipped automatically.

Test data files are located in the testdata/ directory and include:

• Sample FASTA/FASTQ files for sequence format validation
• Sample SAM/BAM files for alignment format validation
• Sample VCF file for variant format validation
• BAM index files for testing random access functionality