bam2bed

This function is used for converting sorted bam file to bed file.

Note

Read1 and read2 will be merged in paired end data.

Parameters

bam2bed(bamInput=None, outputdir=None,
        paired=True, stepNum=None,
        upstream=None)

• bamInput: list, input bam files.

• outputdir: str, output result folder, None means the same folder as input files.

• threads: int, how many thread to use.

• paired: boolean, paired end or single end.

• lenFilter: Whether filter fragment by length, only for paired data.

• minLen: Min fragment length.

• maxLen: Max fragment length.

• stepNum: int or str, step flag for folder name.

• upstream: upstream output results, used for pipeline.

• verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.

Example usage:

bams = ["test1.bam", "test1.bam"]

bam2bed(bamInput=bams)