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Utilities for working with NGS index formats.

Project description

# ngsindex

Support for reading various NGS-related index formats:

* [BAI](https://samtools.github.io/hts-specs/SAMv1.pdf)
* [TBI](https://samtools.github.io/hts-specs/tabix.pdf)
* [CSI](https://samtools.github.io/hts-specs/CSIv2.pdf)

# Installation

```bash
pip install ngsindex
```

# Usage

```python
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:
* https://github.com/samtools/hts-specs/pull/321
* https://github.com/tomwhite/hts-specs/blob/sbi/SAMv1.tex

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