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matOptimize: Allow -D option #386

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Nov 22, 2024
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matOptimize: Allow -D option #386

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5 changes: 4 additions & 1 deletion src/matOptimize/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -283,13 +283,16 @@ int main(int argc, char **argv) {
} else if (input_nh_path!=""&&input_vcf_path!="") {
print_file_info("Load starting tree from", "starting tree file,-t", input_nh_path);
print_file_info("Load sample variant from", "sample vcf,-v", input_vcf_path);
} else if (input_nh_path!=""&&diff_file_path!="") {
print_file_info("Load starting tree from", "starting tree file,-t", input_nh_path);
print_file_info("Load sample variant from", "sample maple/diff,-D", diff_file_path);
}
else {
fputs("Input file not completely specified. Please either \n"
"1. Specify an intermediate protobuf from last run with -a to continue optimization, or\n"
"2. Specify a usher-compatible protobuf with -i, and both starting tree and sample variants will be extracted from it, or\n"
"3. Specify a usher-compatible protobuf with -i for starting tree, and a VCF with -v for sample variants, or\n"
"4. Specify the starting tree in newick format with -t, and a VCF with -v for sample variants.\n",stderr);
"4. Specify the starting tree in newick format with -t, and either a VCF with -v or a Maple/diff with -D for sample variants.\n",stderr);
std::cerr << desc << std::endl;
exit(EXIT_FAILURE);
}
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