FGBIO SETMATEINFORMATION

Adds and/or fixes mate information on paired-end reads. Sets the MQ (mate mapping quality), MC (mate cigar string), ensures all mate-related flag fields are set correctly, and that the mate reference and mate start position are correct.

Example

This wrapper can be used in the following way:

rule SetMateInfo:
    input:
        "mapped/a.bam"
    output:
        "mapped/{sample}.mi.bam"
    params: ""
    log:
        "logs/fgbio/set_mate_info/{sample}.log"
    wrapper:
        "v5.8.0/bio/fgbio/setmateinformation"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

• fgbio=2.4.0

Authors

• Patrik Smeds

Code

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2018, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell

shell.executable("bash")

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

extra_params = snakemake.params.get("extra", "")

bam_input = snakemake.input[0]

if not isinstance(bam_input, str) and len(snakemake.input) != 1:
    raise ValueError("Input bam should be one bam file: " + str(bam_input) + "!")

output_file = snakemake.output[0]

if not isinstance(output_file, str) and len(snakemake.output) != 1:
    raise ValueError("Output should be one bam file: " + str(output_file) + "!")

shell(
    "fgbio SetMateInformation"
    " -i {bam_input}"
    " -o {output_file}"
    " {extra_params}"
    " {log}"
)