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Code Block
all:
        g++ -g -Wall -O2 -I samtools-0.1.6/ BreakDancerMax.cpp AlnParser.cpp Poisson.cpp -o breakdancer_max -lm -L samtools-0.1.6/ -lbam -lz

*Change Changing both the path of the -I and -L flag and also moving the -lz library flag after -lbam.

Congrats! You've, hopefully, installed the CPP portion of Breakdancer. But there is also a Perl script that Breakdancer must run so we need to handle the prerequisites for that.