ngsindex
Support for reading various NGS-related index formats:
Installation
pip install ngsindex
Usage
from ngsindex import IndexType, resolve_index_file, parse_index
from pathlib import Path
bam_file = Path('/path/to/reads.bam')
# Resolve the location of the BAM index file.
index_file = resolve_index_file(bam_file, IndexType.BAI)
# Load the index
index = parse_index(index_file)
# Loop through chromosome indexes
for refidx in index.ref_indexes:
...
Limitations
- CRAM files are not yet supported (neither .crai nor .bai index files).
Todo
- Add support for splitting BAI: