deepbiop.bam

Functions

count_chimeric_reads_for_path(bam[, threads])	Calculate the number of chimeric reads in a BAM file.
count_chimeric_reads_for_paths(bams[, threads])	Calculate the number of chimeric reads in multiple BAM files.
left_right_soft_clip(cigar_string)	Calculate left and right soft clips from a cigar string.

Module Contents

deepbiop.bam.count_chimeric_reads_for_path(bam, threads=None)

Calculate the number of chimeric reads in a BAM file.

Parameters:

• bam (str | os.PathLike | pathlib.Path)

• threads (int | None)

Return type:

int

deepbiop.bam.count_chimeric_reads_for_paths(bams, threads=None)

Calculate the number of chimeric reads in multiple BAM files.

Parameters:

• bams (Sequence[str | os.PathLike | pathlib.Path])

• threads (int | None)

Return type:

dict[pathlib.Path, int]

deepbiop.bam.left_right_soft_clip(cigar_string)

Calculate left and right soft clips from a cigar string.

Parameters:

cigar_string (str)

Return type:

tuple[int, int]