Compilation Errors Tigra-Sv

Question

[roalva1]

Hello I have my sv with breakdancer and I would like to do a local assembly with tigra, but I can not even compile it. I download it from the github version, since I don't have an ubuntu machine neither root access. So I am following the file named INSTALL.md, it is the same as in breakdancer, so when I do make inside of build directory it tells me this:

"tigra-sv/src/exe/tigra-sv/main.cpp:45:18: error: sam.h: No such file or directory"`

Well I solve it by writing hardcode the location of this file in the file named main.cpp. Then, I type make again, and this error doesn't show up, but another one saying this:

main.cpp:(.text+0x8c20): undefined reference to `bgzf_tell'

I can't figure out what to do after googling it.

could you help me please?

Thanks!

Answer 1

[Istvan Albert]

make sure to add the path to the whole samtools as a library in the makefile and don't just edit a single file. It is probably done with -L and possibly -I flags to the compiler.

As the installation states that:

Since tigra_sv uses samtools C API. Please install samtools (http://samtools.sourceforge.net/). Please also modify the Makefile to link the compiler to the correct locations of samtools in your system.

Answer 2

[Liyf]

Roalva, I get the same problem. And I even cannot install breakdancer, would you please help me about breakdancer? And this problem?