gcc -g -Wall -O2 -I.. calDepth.c -o $@ -lm -lz -L.. -lbam
clean:
- rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf
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+ rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf
+
+# ../samtools pileup ex1.bam|perl -ape '$_=$F[4];s/\^.//g;$x=tr/A-Z/X/;$y=tr/a-z/x/;s/(\d+)(X)/$x-=$1,$2/eg;s/(\d+)(x)/$y-=$1,$2/eg;$_=join("\t",@F[0,1],$x,$y)."\n"'
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