-all: ex1.glf ex1.pileup.gz ex1.bam.bai ex1.glfview.gz \
+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 ex8.bam.bai \
+ ex9_nofail.bam.bai \
+ ex9_fail.bam.bai \
+ ex10.bam ex10.bam.bai
ex2.sam.gz: ex1.bam ex1.bam.bai
samtools view -h ex1.bam | gzip > ex2.sam.gz
samtools index $<
ex1.pileup.gz:ex1.bam ex1.fa
samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
-ex1.glf:ex1.bam ex1.fa
- samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-ex1.glfview.gz:ex1.glf
- samtools glfview ex1.glf | gzip > ex1.glfview.gz
clean:
- rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM pysam_*.sam ex2.sam ex2.sam.gz ex1.sam
+ rm -fr *.bam *.bai *.fai *.pileup* \
+ *~ calDepth *.dSYM pysam_*.sam \
+ ex2.sam ex2.sam.gz ex1.sam