all: ex1.pileup.gz ex1.bam.bai \
	ex2.sam.gz ex2.sam ex1.sam \
	ex2.bam \
	ex3.bam ex3.bam.bai \
	ex4.bam ex4.bam.bai \
	ex5.bam ex5.bam.bai \
	ex6.bam \
	ex8.bam ex8.bam.bai \
	ex9_nofail.bam.bai \
	ex9_fail.bam.bai \
        ex10.bam ex10.bam.bai \
	example_unmapped_reads_no_sq.bam \
	example_user_header.bam \
	example_btag.bam

ex2.sam.gz: ex1.bam ex1.bam.bai
		samtools view -h ex1.bam | gzip > ex2.sam.gz

%.bam: %.sam ex1.fa.fai
	samtools import ex1.fa.fai $< $@

%.sam: %.sam.gz
	gunzip < $< > $@

ex1.fa.fai:ex1.fa
		samtools faidx ex1.fa
ex1.bam:ex1.sam.gz ex1.fa.fai
		samtools import ex1.fa.fai ex1.sam.gz ex1.bam
%.bam.bai:%.bam
		samtools index $<
ex1.pileup.gz:ex1.bam ex1.fa
		samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz

example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam
	touch tmp.list
	samtools import tmp.list $< $@
	rm -f tmp.list

clean:
	rm -fr *.bam *.bai *.fai *.pileup* \
		*~ calDepth *.dSYM pysam_*.sam \
	ex2.sam ex2.sam.gz ex1.sam