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apcamargo authored Dec 20, 2024
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<h1 align="center">pyCoverM</h1>

pyCoverM is a Python library that provides a simple interface to [CoverM](https://github.com/wwood/CoverM) for fast coverage estimation.
pyCoverM is a Python library that provides bindings to [CoverM](https://github.com/wwood/CoverM), enabling fast coverage estimation.

## Installation

pyCoverM is available through PyPI or Conda.
pyCoverM is available via PyPI or Conda.

### PyPI installation

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mamba activate pycoverm_env
```

### Quick start
## Quick start

pyCoverM provides two functions:
1. `is_bam_sorted` - Verifies if a BAM file is sorted by coordinate.
2. `get_coverages_from_bam` - Computes average contig coverages from sorted BAM files.
1. `is_bam_sorted`: Checks if a BAM file is sorted by coordinate and returns `True` if sorted, or `False` otherwise.
2. `get_coverages_from_bam`: Computes the average contig coverage from sorted BAM files. It returns a tuple where the first element is a list of contig names, and the second is a NumPy array of coverage values.

### Example usage

```py
>>> import pycoverm
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