HiCQCAnalyzer


class chr3d.HiCQCAnalyzer()

Quality control analyzer for Hi-C data.

Parses and summarizes QC metrics from Hi-C pipeline outputs.

Methods


def analyze(
    self,
    qc_dir: str,
    output_dir: str,
) -> Dict[str, Any]

Analyze QC metrics from pipeline outputs.

Parameters:

Parameter	Type	Description
qc_dir	`str`	Path to QC directory
output_dir	`str`	Output directory for summary


def parse_alignment_stats(
    self,
    stats_file: str,
) -> Dict[str, Any]

Parse samtools stats output file.

Parameters:

Parameter	Type	Description
stats_file	`str`	Path to samtools stats file

Example:


import chr3d as c3d
 
qc = c3d.HiCQCAnalyzer()
stats = qc.analyze(qc_dir="results/qc", output_dir="results/summary")