1 all: ex1.pileup.gz ex1.bam.bai \
2 ex2.sam.gz ex2.sam ex1.sam \
13 ex2.sam.gz: ex1.bam ex1.bam.bai
14 samtools view -h ex1.bam | gzip > ex2.sam.gz
16 %.bam: %.sam ex1.fa.fai
17 samtools import ex1.fa.fai $< $@
24 ex1.bam:ex1.sam.gz ex1.fa.fai
25 samtools import ex1.fa.fai ex1.sam.gz ex1.bam
28 ex1.pileup.gz:ex1.bam ex1.fa
29 samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
32 rm -fr *.bam *.bai *.fai *.pileup* \
33 *~ calDepth *.dSYM pysam_*.sam \
34 ex2.sam ex2.sam.gz ex1.sam