Mercurial > repos > siyuan > prada
view pyPRADA_1.2/tools/samtools-0.1.16/examples/Makefile @ 3:f17965495ec9 draft default tip
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author | siyuan |
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date | Tue, 11 Mar 2014 12:14:01 -0400 |
parents | acc2ca1a3ba4 |
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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 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 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) ../libbam.a: (cd ..; make libbam.a) calDepth:../libbam.a calDepth.c 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/(\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"'