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