-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
../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)
(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"'