Revert one of my earlier changes - Heng was right, CIGAR P not sensible in a padded...

[samtools.git] / examples / Makefile

diff --git a/examples/Makefile b/examples/Makefile
index 2733a573ffbecc5a33599bb9e7425b7f9d3be994..309399f3affae42e494903604243d36a11c16f3d 100644 (file)
--- 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"'