-all:../libbam.a ../samtools ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz calDepth
+all:../libbam.a ../samtools ../bcftools/bcftools \
+ ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz ex1.bcf calDepth
@echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;
ex1.fa.fai:ex1.fa
ex1f-rmdupse.bam:ex1f.bam
../samtools rmdup -S ex1f.bam $@
+ex1.bcf:ex1.bam ex1.fa.fai
+ ../samtools mpileup -gf ex1.fa ex1.bam > $@
+
+../bcftools/bcftools:
+ (cd ../bcftools; make bcftools)
+
../samtools:
(cd ..; make samtools)
gcc -g -Wall -O2 -I.. calDepth.c -o $@ -lm -lz -L.. -lbam
clean:
- rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg
\ No newline at end of file
+ rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf
\ No newline at end of file