X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=examples%2FMakefile;h=309399f3affae42e494903604243d36a11c16f3d;hp=3fe3e5a63a8643c49e8bf75447d4a55fac847add;hb=0f906dafb2ad22371a753557562ef95c3034480d;hpb=b27e00385f41769d03a8cca4dbd71275fc9fa906

diff --git a/examples/Makefile b/examples/Makefile
index 3fe3e5a..309399f 100644
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -1,4 +1,5 @@
-all:../libbam.a ../samtools ex1.glf ex1.pileup.gz ex1.bam.bai 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
@@ -13,6 +14,24 @@ ex1.glf:ex1.bam ex1.fa
 		../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
 ex1.glfview.gz:ex1.glf
 		../samtools glfview ex1.glf | gzip > ex1.glfview.gz
+ex1a.bam:ex1.bam
+		../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view -bS - > $@
+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	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
+		../samtools rmdup ex1f.bam $@
+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)
@@ -21,7 +40,11 @@ ex1.glfview.gz:ex1.glf
 		(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
\ No newline at end of file
+		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"'
+
+# ../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"'