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Selectsites input file type #121

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Merged
masarunakajima merged 2 commits into from
Aug 30, 2023
Merged

Selectsites input file type #121

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0c7c3f1
selectsites: testing if the input file is compressed and if it is the…
andrewdavidsmith Aug 30, 2023
43639de
Merge branch 'master' of github.com:smithlabcode/dnmtools into select…
andrewdavidsmith Aug 30, 2023
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18 changes: 18 additions & 0 deletions src/utils/selectsites.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -159,11 +159,23 @@ regions_by_chrom(vector<GenomicRegion> &regions,
regions.shrink_to_fit();
}


inline bool
file_exists(const string &filename) {
return (access(filename.c_str(), F_OK) == 0);
}


static bool
is_compressed_file(const string &filename) {
const bgzf_file f(filename.c_str(), "r");
htsFormat fmt;
const int ret = hts_detect_format(f.f->fp, &fmt);
if (ret != 0) throw runtime_error("failed to detect format: " + filename);
return fmt.compression != no_compression;
}


int
main_selectsites(int argc, const char **argv) {

Expand Down Expand Up @@ -215,6 +227,12 @@ main_selectsites(int argc, const char **argv) {
if (isdir(sites_file.c_str()) || !file_exists(sites_file))
throw runtime_error("bad input sites file: " + sites_file);

if (is_compressed_file(sites_file)) {
LOAD_ENTIRE_FILE = true;
if (VERBOSE)
cerr << "input file is so must be loaded" << endl;
}

vector<GenomicRegion> regions;
ReadBEDFile(regions_file, regions);
if (!check_sorted(regions))
Expand Down