gtars-igd
Implementation of IGD (Integrated Genome Database) - a high-performance genomic interval search tool.
Features
- Fast interval queries (logarithmic time complexity)
- Memory-efficient indexing
- Binary format for persistence
- Support for multiple genomes
Usage
Ensure gtars
is compiled with igd:
cargo build --release --all-features
or cargo build --release --features igd
Building an Index
gtars igd create --output /home/igd_output/ --filelist /home/my_bedfiles/
Querying with a single bed file
gtars igd search --database my_igd_database.igd --query my_query.bed
Performance
- Index creation: O(n log n)
- Query time: O(log n + k) where k is number of results
- Memory usage: ~30% of input file size
File Format
IGD uses a binary format optimized for:
- Fast loading
- Compact storage
- Memory-mapped access