This package includes tools for creating and manipulating GBAM files. GBAM is a new column oriented file format for storing binary alignment data. The way it stores information allows to skip unnecessary operations which are inevitable when using regular BAM files.
git clone https://github.com/NickRoz1/gbam
cd gbam
cargo build --release
./target/release/gbam_binary --helpYou may need to install following packages:
sudo apt-get install liblzma-dev
sudo apt-get install libbz2-dev# Simply convert
time ./target/release/gbam_binary -c test.bam -o test.gbam
# Sort before writing (sort by reference and coordinates (other sort predicates are available, but not implemented in CLI currently))
time ./target/release/gbam_binary -c -s 1gb.bam -o 1gb.sorted.gbam --sort-temp-mode [lz4_file|file|lz4_ram|ram]
# Collect flag statistics
time ./target/release/gbam_binary --flagstat test.gbam
# Calculate read depth (only on sorted files)
time ./target/release/gbam_binary --depth test.sorted.gbam --thread-num 4 > depth_test.txt
# Calculate read depth (only on sorted files) and create bed regions depth gzip file
time ./target/release/gbam_binary --depth test.sorted.gbam --thread-num 4 -o test_data/depth_test.bed.gz# Run all tests
pytest
# To run all correctness test on a specific file path
pytest --use-custom-file=/home/test/testing_big_file/test.bam
# Test sort on user provided file (slow)
pytest -k test_sort --bam-file-path=/home/test/testing_big_file/test.bam
# Test conversion bam to gbam to bam (preserving correct data) on user provided file
pytest -k test_bam_to_gbam_to_bam --bam-file-path=/home/test/testing_big_file/test.bamSee benchmarks
Data is available for download.
GNU Guix provides a full environment for development. See .guix-build