1 --- a/examples/Makefile
2 +++ b/examples/Makefile
4 all:../libbam.a ../samtools ../bcftools/bcftools \
5 - ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz ex1.bcf calDepth
6 + ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.bcf calDepth
7 @echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;
11 ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
13 ../samtools index ex1.bam
14 -ex1.pileup.gz:ex1.bam ex1.fa
15 - ../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
16 -ex1.glf:ex1.bam ex1.fa
17 - ../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
18 -ex1.glfview.gz:ex1.glf
19 - ../samtools glfview ex1.glf | gzip > ex1.glfview.gz
21 ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view -bS - > $@