seqonly/src/__init__.py

"""SV-SPR: Short-read SV confidence model (caller-agnostic post-VCF rescoring).

Quick start
-----------
    >>> from svspr import score, classify, SVSPR
    >>>
    >>> # Single SV
    >>> classify(chrom='chr1', pos=12345, end=13345,
    ...         svtype='DEL', svlen=1000, total_alt_support=15)
    {'CS': 0.87, 'tier': 'high'}
    >>>
    >>> # Full VCF
    >>> df = score(vcf_path='input.vcf', ref_path='GRCh38.fa')
    >>> df[['chrom', 'pos', 'svtype', 'CS', 'tier']].head()
"""
from .model import SVSPR, score, classify, load_default
from .features import SVCall, FEATURE_COLS, extract_one, extract_batch, from_vcf

__version__ = '0.1.0'
__all__ = ['SVSPR', 'score', 'classify', 'load_default',
           'SVCall', 'FEATURE_COLS', 'extract_one', 'extract_batch', 'from_vcf']