X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=examples%2FMakefile;h=8f0386fcaa48730dc24a276546cbe377ffffc756;hp=3fe3e5a63a8643c49e8bf75447d4a55fac847add;hb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a

diff --git a/examples/Makefile b/examples/Makefile
index 3fe3e5a..8f0386f 100644
--- a/examples/Makefile
+++ b/examples/Makefile
@@ -1,4 +1,4 @@
-all:../libbam.a ../samtools ex1.glf ex1.pileup.gz ex1.bam.bai ex1.glfview.gz calDepth
+all:../libbam.a ../samtools ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz calDepth
 		@echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;
 
 ex1.fa.fai:ex1.fa
@@ -13,6 +13,18 @@ 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"; echo "@RG	ID:ex1a	LB:ex1"; echo "@RG	ID:ex1b	LB: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 $@
 
 ../samtools:
 		(cd ..; make samtools)
@@ -24,4 +36,4 @@ calDepth:../libbam.a calDepth.c
 		gcc -g -Wall -O2 -I.. calDepth.c -o $@ -lm -lz -L.. -lbam
 
 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
\ No newline at end of file