1 all:../samtools ex1.glf ex1.pileup.gz ex1.bam.bai ex1.glfview.gz
2 @echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;
5 ../samtools faidx ex1.fa
6 ex1.bam:ex1.sam.gz ex1.fa.fai
7 ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
9 ../samtools index ex1.bam
10 ex1.pileup.gz:ex1.bam ex1.fa
11 ../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
12 ex1.glf:ex1.bam ex1.fa
13 ../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
14 ex1.glfview.gz:ex1.glf
15 ../samtools glfview ex1.glf | gzip > ex1.glfview.gz
18 (cd ..; make samtools)
21 rm -f *.bam *.bai *.glf* *.fai *.pileup* *~