HiCSamProcessor


class chr3d.HiCSamProcessor(
    threads: int = 1,
    min_mapq: int = 30,
)

SAM/BAM processing for Hi-C data using samtools.

Converts SAM to BAM and sorts by read name (required for pairtools).

Parameters

Parameter	Type	Description
threads	`int`	Number of threads for samtools (default: 1)
min_mapq	`int`	Minimum mapping quality score (default: 30)

Methods

process


def process(
    self,
    input_sam: str,
    output_bam: str,
    stats_file: Optional[str] = None,
    keep_unsorted: bool = False,
) -> Dict[str, Any]

Convert SAM to sorted BAM.

Parameters:

Parameter	Type	Description
input_sam	`str`	Path to input SAM file
output_bam	`str`	Path to output sorted BAM file
stats_file	`Optional[str]`	Optional path to save BAM stats
keep_unsorted	`bool`	Keep unsorted BAM file (default: `False`)

Returns:

Dict[str, Any] with keys:

'output_bam': Path to output BAM file
'stats_file': Path to stats file
'bam_size_bytes': Size of BAM file in bytes

Example:


import chr3d as c3d
 
processor = c3d.HiCSamProcessor(threads=24, min_mapq=30)
 
stats = processor.process(
    input_sam="aligned.sam",
    output_bam="sorted.bam"
)