Compiling the code - Githubissues

Hi guys, thanks for sharing your tool, I enjoyed reading your paper on the archive. I'd like to test your BAF approach to identify breakpoints on our single-cell data but run into issues compiling the BAFExtract tool.

"make: Warning: File `Makefile' has modification time 4.4e+02 s in the future g++ -c -Wall -O3 main.cpp -o main.o main.cpp:304:10: error: 't_mapped_PE_read' was not declared in this scope vector<t_mapped_PE_read> first_mate_reads, ^ main.cpp:304:27: error: template argument 1 is invalid vector<t_mapped_PE_read> first_mate_reads, ^ main.cpp:304:27: error: template argument 2 is invalid main.cpp:304:10: error: 't_mapped_PE_read' was not declared in this scope vector<t_mapped_PE_read> first_mate_reads, ^ main.cpp:304:27: error: template argument 1 is invalid vector<t_mapped_PE_read> first_mate_reads, ^ main.cpp:304:27: error: template argument 2 is invalid main.cpp:304:3: error: 'vector' is not a type vector<t_mapped_PE_read> first_mate_reads, ^ main.cpp:304:9: error: expected ',' or '...' before '<' token vector<t_mapped_PE_read> first_mate_reads, ^ main.cpp: In function 'void dump_nucleotide_pileup_per_SAM_file(char, std::vector<char>, std::vector, char, int, int, int&)': main.cpp:617:144: warning: format '%d' expects a matching 'int' argument [-Wformat=] fprintf(stderr, "Loaded pileup is not the same length as the chromosome info: %s: %d, %d\n", chr_ids->at(i_chr), chr_lengths->at(i_chr)); ^ main.cpp: In function 'int main(int, char)': main.cpp:976:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i_chr = 0; i_chr < chr_ids->size(); i_chr++) ^ main.cpp:1012:64: warning: array subscript has type 'char' [-Wchar-subscripts] bool is_alternate_allele = (nuc_2_num_array[cur_chr_seq[i]] != i_all); ^ make: [main.o] Error 1"

Hope you have some advice. Thanks!

Soren

akdess / BAFExtract

Compiling the code #1