Mercurial > repos > siyuan > prada
comparison pyPRADA_1.2/tools/samtools-0.1.16/examples/Makefile @ 0:acc2ca1a3ba4
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| author | siyuan |
|---|---|
| date | Thu, 20 Feb 2014 00:44:58 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:acc2ca1a3ba4 |
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| 1 all:../libbam.a ../samtools ../bcftools/bcftools \ | |
| 2 ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz ex1.bcf calDepth | |
| 3 @echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo; | |
| 4 | |
| 5 ex1.fa.fai:ex1.fa | |
| 6 ../samtools faidx ex1.fa | |
| 7 ex1.bam:ex1.sam.gz ex1.fa.fai | |
| 8 ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam | |
| 9 ex1.bam.bai:ex1.bam | |
| 10 ../samtools index ex1.bam | |
| 11 ex1.pileup.gz:ex1.bam ex1.fa | |
| 12 ../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz | |
| 13 ex1.glf:ex1.bam ex1.fa | |
| 14 ../samtools pileup -gf ex1.fa ex1.bam > ex1.glf | |
| 15 ex1.glfview.gz:ex1.glf | |
| 16 ../samtools glfview ex1.glf | gzip > ex1.glfview.gz | |
| 17 ex1a.bam:ex1.bam | |
| 18 ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view -bS - > $@ | |
| 19 ex1b.bam:ex1.bam | |
| 20 ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"b";print}}' | ../samtools view -bS - > $@ | |
| 21 ex1f.rg: | |
| 22 (echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > $@ | |
| 23 ex1f.bam:ex1.bam ex1a.bam ex1b.bam ex1f.rg | |
| 24 ../samtools merge -rh ex1f.rg $@ ex1.bam ex1a.bam ex1b.bam | |
| 25 ex1f-rmduppe.bam:ex1f.bam | |
| 26 ../samtools rmdup ex1f.bam $@ | |
| 27 ex1f-rmdupse.bam:ex1f.bam | |
| 28 ../samtools rmdup -S ex1f.bam $@ | |
| 29 | |
| 30 ex1.bcf:ex1.bam ex1.fa.fai | |
| 31 ../samtools mpileup -gf ex1.fa ex1.bam > $@ | |
| 32 | |
| 33 ../bcftools/bcftools: | |
| 34 (cd ../bcftools; make bcftools) | |
| 35 | |
| 36 ../samtools: | |
| 37 (cd ..; make samtools) | |
| 38 | |
| 39 ../libbam.a: | |
| 40 (cd ..; make libbam.a) | |
| 41 | |
| 42 calDepth:../libbam.a calDepth.c | |
| 43 gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz | |
| 44 | |
| 45 clean: | |
| 46 rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf | |
| 47 | |
| 48 # ../samtools pileup ex1.bam|perl -ape '$_=$F[4];s/(\d+)(??{".{$1}"})|\^.//g;@_=(tr/A-Z//,tr/a-z//);$_=join("\t",@F[0,1],@_)."\n"' | |
| 49 | |
| 50 # ../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"' |