1 all:../libbam.a ../samtools ex1.glf ex1.pileup.gz ex1.bam.bai ex1f-rmduppe.bam ex1f-rmdupse.bam ex1.glfview.gz calDepth
2 @echo; echo \# You can now launch the viewer with: \'samtools tview ex1.bam ex1.fa\'; echo;
5 ../samtools faidx ex1.fa
6 ex1.bam:ex1.sam.gz ex1.fa.fai
7 ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
9 ../samtools index ex1.bam
10 ex1.pileup.gz:ex1.bam ex1.fa
11 ../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
12 ex1.glf:ex1.bam ex1.fa
13 ../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
14 ex1.glfview.gz:ex1.glf
15 ../samtools glfview ex1.glf | gzip > ex1.glfview.gz
17 ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"a";print}}' | ../samtools view -bS - > $@
19 ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$$1=$$1"b";print}}' | ../samtools view -bS - > $@
21 (echo "@RG ID:ex1 LB:ex1"; echo "@RG ID:ex1a LB:ex1"; echo "@RG ID:ex1b LB:ex1b") > $@
22 ex1f.bam:ex1.bam ex1a.bam ex1b.bam ex1f.rg
23 ../samtools merge -rh ex1f.rg $@ ex1.bam ex1a.bam ex1b.bam
24 ex1f-rmduppe.bam:ex1f.bam
25 ../samtools rmdup ex1f.bam $@
26 ex1f-rmdupse.bam:ex1f.bam
27 ../samtools rmdup -S ex1f.bam $@
30 (cd ..; make samtools)
33 (cd ..; make libbam.a)
35 calDepth:../libbam.a calDepth.c
36 gcc -g -Wall -O2 -I.. calDepth.c -o $@ -lm -lz -L.. -lbam
39 rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg