Extract unique mapped blocks and compile error

[Yudi Zhang]

Hi there,

 

I have an error when I was trying compile it:

/home/yudiz/local/bpp/dev/sources/jydu-maffilter-c975f4d/MafFilter/MafFilter.cpp: In function ‘int main(int, char**)’:

/home/yudiz/local/bpp/dev/sources/jydu-maffilter-c975f4d/MafFilter/MafFilter.cpp:1219:59: error: ‘class bpp::BppOSubstitutionModelFormat’ has no member named ‘read’

 1219 |           unique_ptr<SubstitutionModel> model(modelReader.read(&AlphabetTools::DNA_ALPHABET, modelDesc, 0, true));

      |                                                           ^~~~

make[2]: *** [MafFilter/CMakeFiles/maffilter.dir/build.make:63: MafFilter/CMakeFiles/maffilter.dir/MafFilter.cpp.o] Error 1

make[1]: *** [CMakeFiles/Makefile2:197: MafFilter/CMakeFiles/maffilter.dir/all] Error 2

make: *** [Makefile:152: all] Error 2

Could you please tell me how to fix this? Thanks.

Also, I want to use maffiler to extract unique mapped alignment based on my 2 aligned genomes, i.e the region in one genome A can only be aligned to the region in another genome B, same for genome B, can I use subset to do this?

Best,

Z

[Julien Y. Dutheil]

Dear Yudi

Regarding the compilation issue: it should be fixed now. To be 100% sure to get a compilable version it is recommended to get the stable version of both maffilter and the Bio++ libraries. The development version (master branch) can occasionally breakdown as we're developing the Bio++ libraries upstream.

Regarding duplicates: the Subset filter can only discard blocks where one species is present multiple times, such as:

sp1.chr1 .......

sp2.chr1 ......

sp2.chr2 ......

But it cannot identify cases where a single sequence is present in multiple blocks.

Best,

Julien.

[Yudi Zhang]

Hi Julien,

Thanks for answering that! I also downloaded mafFilter from condo: https://anaconda.org/bioconda/ucsc-maffilter, is it the same?

There is one argument called -overlap - Reject overlapping blocks in reference (assumes ordered blocks). Is it the one I want?  

Thanks,

Yudi

[Julien Y. Dutheil]

Hi,

Sorry, I'm only seeing this now... ucsc-maffilter is a distinct program, unrelated to MafFilter. I'm not sure what the -overlap options does, but it might be worth giving a look.

Julien.