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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
../samtools faidx ex1.fa
ex1.bam:ex1.sam.gz ex1.fa.fai
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
ex1.bam.bai:ex1.bam
../samtools index ex1.bam
ex1.pileup.gz:ex1.bam ex1.fa
../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
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)
../libbam.a:
(cd ..; make libbam.a)
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 ex1*.rg
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