1 all: ex1.glf ex1.pileup.gz ex1.bam.bai ex1.glfview.gz \
2 ex2.sam.gz ex2.sam ex1.sam \
9 ex2.sam.gz: ex1.bam ex1.bam.bai
10 samtools view -h ex1.bam | gzip > ex2.sam.gz
12 %.bam: %.sam ex1.fa.fai
13 samtools import ex1.fa.fai $< $@
20 ex1.bam:ex1.sam.gz ex1.fa.fai
21 samtools import ex1.fa.fai ex1.sam.gz ex1.bam
24 ex1.pileup.gz:ex1.bam ex1.fa
25 samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
26 ex1.glf:ex1.bam ex1.fa
27 samtools pileup -gf ex1.fa ex1.bam > ex1.glf
28 ex1.glfview.gz:ex1.glf
29 samtools glfview ex1.glf | gzip > ex1.glfview.gz
32 rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM pysam_*.sam ex2.sam ex2.sam.gz ex1.sam