X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=examples%2FMakefile;h=309399f3affae42e494903604243d36a11c16f3d;hb=607d7a0ab79152be4153fa09861cfa889488f2c7;hp=2733a573ffbecc5a33599bb9e7425b7f9d3be994;hpb=d14782f26230244039bf38f6384a7a9106b0daed;p=samtools.git

diff --git a/examples/Makefile b/examples/Makefile
index 2733a57..309399f 100644
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -40,9 +40,11 @@ ex1.bcf:ex1.bam ex1.fa.fai
 		(cd ..; make libbam.a)
 
 calDepth:../libbam.a calDepth.c
-		gcc -g -Wall -O2 -I.. calDepth.c -o $@ -lm -lz -L.. -lbam
+		gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz
 
 clean:
 		rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf
 
-# ../samtools pileup ex1.bam|perl -ape '$_=$F[4];s/(\d+)(??{".{$1}"})|\^.//g;@_=(tr/A-Z//,tr/a-z//);$_=join("\t",@F[0,1],@_)."\n"'
\ No newline at end of file
+# ../samtools pileup ex1.bam|perl -ape '$_=$F[4];s/(\d+)(??{".{$1}"})|\^.//g;@_=(tr/A-Z//,tr/a-z//);$_=join("\t",@F[0,1],@_)."\n"'
+
+# ../samtools pileup -cf ex1.fa ex1.bam|perl -ape '$_=$F[8];s/\^.//g;s/(\d+)(??{".{$1}"})|\^.//g;@_=(tr/A-Za-z//,tr/,.//);$_=join("\t",@F[0,1],@_)."\n"'