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Verbose output for sym and xcounts #227

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Jun 8, 2024
Merged

Verbose output for sym and xcounts #227

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12 changes: 7 additions & 5 deletions src/utils/symmetric-cpgs.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,7 @@ get_first_site(T &in, T &out) {
}

template<class T> static bool
process_sites(T &in, T &out) {
process_sites(const bool verbose, T &in, T &out) {

// get the first site while dealing with the header
auto [prev_site, prev_is_cpg] = get_first_site(in, out);
Expand All @@ -101,6 +101,8 @@ process_sites(T &in, T &out) {
}
}
else {
if (verbose)
cerr << "processing: " << curr_site.chrom << endl;
if (chroms_seen.find(curr_site.chrom) != cend(chroms_seen)) return false;
chroms_seen.insert(curr_site.chrom);

Expand All @@ -125,7 +127,7 @@ main_symmetric_cpgs(int argc, const char **argv) {
try {
// file types from HTSlib use "-" for the filename to go to stdout
string outfile{"-"};
// (not used) bool VERBOSE = false;
bool verbose = false;
bool compress_output = false;
int32_t n_threads = 1;

Expand All @@ -139,7 +141,7 @@ main_symmetric_cpgs(int argc, const char **argv) {
outfile);
opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
opt_parse.add_opt("zip", 'z', "output gzip format", false, compress_output);
// opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
opt_parse.add_opt("verbose", 'v', "print more run info", false, verbose);
std::vector<string> leftover_args;
opt_parse.parse(argc, argv, leftover_args);
if (argc == 1 || opt_parse.help_requested()) {
Expand Down Expand Up @@ -179,11 +181,11 @@ main_symmetric_cpgs(int argc, const char **argv) {
tp.set_io(out);
}

const bool sites_are_sorted = process_sites(in, out);
const bool sites_are_sorted = process_sites(verbose, in, out);

if (!sites_are_sorted) {
namespace fs = std::filesystem;
cerr << "sites are not sorted in: " << filename << endl;
namespace fs = std::filesystem;
const fs::path outpath{outfile};
if (fs::exists(outpath)) fs::remove(outpath);
return EXIT_FAILURE;
Expand Down
14 changes: 8 additions & 6 deletions src/utils/xcounts.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,7 @@ fill_output_buffer(const uint32_t offset, const MSite &s, T &buf) {
int
main_xcounts(int argc, const char **argv) {
try {
bool verbose = false;
bool require_coverage = false;
size_t n_threads = 1;
string genome_file;
Expand All @@ -104,6 +105,7 @@ main_xcounts(int argc, const char **argv) {
false, header_file);
opt_parse.add_opt("threads", 't', "threads for compression (use few)",
false, n_threads);
opt_parse.add_opt("verbose", 'v', "print more run info", false, verbose);
std::vector<string> leftover_args;
opt_parse.parse(argc, argv, leftover_args);
if (argc == 1 || opt_parse.help_requested()) {
Expand Down Expand Up @@ -132,20 +134,18 @@ main_xcounts(int argc, const char **argv) {
const int ret =
get_chrom_sizes_for_counts_header(n_threads, genome_file,
chrom_names, chrom_sizes);
if (ret) throw dnmt_error("failed to get chrom sizes from: " +
genome_file);
if (ret)
throw dnmt_error{"failed to get chrom sizes from: " + genome_file};
}


bamxx::bam_tpool tpool(n_threads);

bgzf_file in(filename, "r");
if (!in) throw dnmt_error("could not open file: " + filename);
if (!in) throw dnmt_error{"could not open file: " + filename};

const auto outfile_mode = in.is_compressed() ? "w" : "wu";

bgzf_file out(outfile, outfile_mode);
if (!out) throw dnmt_error("error opening output file: " + outfile);
if (!out) throw dnmt_error{"error opening output file: " + outfile};

if (n_threads > 1) {
if (in.is_bgzf())
Expand Down Expand Up @@ -184,6 +184,8 @@ main_xcounts(int argc, const char **argv) {
if (!status_ok || !found_header) break;

if (site.chrom != prev_chrom) {
if (verbose)
cerr << "processing: " << site.chrom << endl;
prev_chrom = site.chrom;
offset = 0;

Expand Down
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