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For both apex cis and apex store, the output files returned were different than those described in the documentation pages, but they matched those in the source code, e.g.

apex/src/cisMapping.cpp

Lines 75 to 77 in 63b605e

std::string block_file_path = global_opts::out_prefix + "." + "cis_sumstats" + ".txt.gz";
std::string bed_block_file_path = global_opts::out_prefix + "." + "cis_gene_table" + ".txt.gz";
std::string long_file_path = global_opts::out_prefix + "." + "cis_long_table" + ".txt.gz";

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