import smbl
import rnftools

# CONFIGURATION

reference = smbl.fasta.EXAMPLE_1
reads = "reads.fq"

# READ SIMULATION

rnftools.mishmash.sample(reads[:-3],reads_in_tuple=1)

rnftools.mishmash.DwgSim(
	fasta=reference,
	read_length_1=100,
	read_length_2=0,
	number_of_read_tuples=10000
)

# ALIGNMENTS

alignments = [
		smbl.prog.BwaMem(
			fasta=reference,
			fastq_1=reads,
			bam="BWA-MEM.bam",
		),

		smbl.prog.Yara(
			fasta=reference,
			fastq_1=reads,
			bam="YARA.bam",
		),
	]


# SNAKEMAKE RULES

rule basic:
	input: [aln.bam_fn() for aln in alignments]
include: rnftools.include()
