HiCAligner


class chr3d.HiCAligner(
    genome_index: str,
    threads: int = 1,
)

Hi-C alignment using BWA MEM with Hi-C specific parameters.

Uses BWA MEM with -SP5M flags optimized for Hi-C chimeric reads.

Parameters

Parameter	Type	Description
genome_index	`str`	Path to BWA-indexed genome FASTA
threads	`int`	Number of threads for BWA (default: 1)

Methods

align


def align(
    self,
    fastq1: str,
    fastq2: str,
    output_sam: str,
    stats_file: Optional[str] = None,
) -> Dict[str, Any]

Run BWA MEM alignment for Hi-C data.

Parameters:

Parameter	Type	Description
fastq1	`str`	Path to R1 FASTQ file
fastq2	`str`	Path to R2 FASTQ file
output_sam	`str`	Path to output SAM file
stats_file	`Optional[str]`	Optional path to save alignment stats

Returns:

Dict[str, Any] with keys:

'output_sam': Path to output SAM file
'stats_file': Path to stats file
'sam_size_bytes': Size of SAM file in bytes

Example:


import chr3d as c3d
 
aligner = c3d.HiCAligner(
    genome_index="/data/genomes/hg38.fa",
    threads=24
)
 
stats = aligner.align(
    fastq1="sample_R1.fastq.gz",
    fastq2="sample_R2.fastq.gz",
    output_sam="aligned.sam"
)