X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=examples%2FMakefile;h=309399f3affae42e494903604243d36a11c16f3d;hb=3a1bd4d97b4d58148b5a7fd845a3b6a023eecbed;hp=b12f882e1fd3cb9fd92dbd9909df11167943716c;hpb=6df2741e66faa911a11f38a5ee1c42c1f1a523ef;p=samtools.git

diff --git a/examples/Makefile b/examples/Makefile
index b12f882..309399f 100644
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -19,7 +19,7 @@ ex1a.bam:ex1.bam
 ex1b.bam:ex1.bam
 		../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"b";print}}' | ../samtools view -bS - > $@
 ex1f.rg:
-		(echo "@RG	ID:ex1	LB:ex1"; echo "@RG	ID:ex1a	LB:ex1"; echo "@RG	ID:ex1b	LB:ex1b") > $@
+		(echo "@RG	ID:ex1	LB:ex1	SM:ex1"; echo "@RG	ID:ex1a	LB:ex1	SM:ex1"; echo "@RG	ID:ex1b	LB:ex1b	SM:ex1b") > $@
 ex1f.bam:ex1.bam ex1a.bam ex1b.bam ex1f.rg
 		../samtools merge -rh ex1f.rg $@ ex1.bam ex1a.bam ex1b.bam
 ex1f-rmduppe.bam:ex1f.bam
@@ -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/\^.//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"'
\ 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"'