Align

class bsbolt.Align.BisulfiteAlignmentAndProcessing(alignment_commands, output=None, output_threads=1, output_to_stdout=False)

Read alignment as processing. Handles reads from BWA-MEM2 and outputs to BAM file. Also aggregates alignment stats.

Params:

• alignment_commands (list): bwa alignment commands
• output (str): output prefix
• output_threads (int): number of threads available for bam output
• output_to_stdout (boold): output alignments to stdout

Attributes:

• self.mapping_statistics (dict)*: alignment run statistics

align_reads(self)

Launch bwa alignment. Pipe output to BAM file