Makefile.read_aligner_training

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KHMER=..

KSIZE= 30
HASH_SIZE= 4e8
N_HASHES= 4

all: estimated_probabilities.${KSIZE}.json

my_mock.fa:
	wget https://github.com/dib-lab/khmer-testdata/raw/master/my_mock.fa

%.fastq.gz:
	wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR172/SRR172903/SRR172903.fastq.gz
	wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR172/SRR172902/SRR172902.fastq.gz

combined_reads.ht: SRR172902.fastq.gz SRR172903.fastq.gz
	python $(KHMER)/scripts/load-into-counting.py --ksize $(KSIZE) \
		-x $(HASH_SIZE) -N $(N_HASHES) $@ $^

my_mock.1.bt1: my_mock.fa
	bowtie2-build my_mock.fa my_mock

combined_reads_mapping.bam: SRR172902.fastq.gz SRR172903.fastq.gz my_mock.1.bt1
	bowtie2 -x my_mock -U SRR172902.fastq.gz -U SRR172903.fastq.gz \
		| samtools view -S -F4 -b - > combined_reads_mapping.bam

estimated_probabilities.$(KSIZE).json: combined_reads.ht combined_reads_mapping.bam
	python readaligner_pairhmm_train.py --json combined_reads.ht \
		combined_reads_mapping.bam \
		> estimated_probabilities.${KSIZE}.json