#!/usr/bin/env python

"""

This script performs the Alignment step of the Cancer

Genome Variant pipeline, controlling the processes for

each step.

"""

import sys

import shutil

import bioexcel_align.runbwa as rb

import bioexcel_align.rungatk as rg

import bioexcel_align.alignutils as au

if __name__ == "__main__":

description = ("This script performs the Alignment step of the Cancer "

"Genome Variant pipeline.")

args = au.parse_command_line(description)

if args.bwa_version == 'stable':

pbwa = rb.bwamem_stable(args.bwa_ind_ref, args.threads, args.date,

args.sample, args.files, args.bwadir)

pbwa.wait()

elif args.bwa_version == 'beta':

pbwa = rb.bwamem_beta(args.bwa_ind_ref, args.threads, args.date,

args.sample, args.files, args.bwadir)

pbwa.wait()

else:

sys.exit('No BWA Mem version selected')

psamidx = rb.samtools_index('{0}/{1}.raw.bam'.format(args.bwadir,

args.sample))

psamidx.wait()

pbr = rg.baserecal(args.jvm_opts, args.threads, args.ref,

'{0}/{1}.raw.bam'.format(args.bwadir, args.sample),

args.knownsites, args.gatkdir, args.sample)

pbr.wait()

pab = rg.applybqsr(args.jvm_opts, args.threads,

'{0}/{1}.raw.bam'.format(args.bwadir, args.sample),

args.gatkdir, args.sample)

pab.wait()

shutil.copy('{0}/{1}.final.bam'.format(args.gatkdir, args.sample),

'{0}/{1}.final.bam'.format(args.outdir, args.sample))