Yaml output for bsrate#237

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andrewdavidsmith merged 1 commit into from
Jun 27, 2024
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Yaml output for bsrate #237

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97 changes: 80 additions & 17 deletions src/analysis/bsrate.cpp
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Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,12 @@
* General Public License for more details.
*/

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

#include <bamxx.hpp>

#include <algorithm>
Expand All@@ -28,12 +34,6 @@
#include <unordered_set>
#include <vector>

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

using std::accumulate;
using std::cerr;
using std::cout;
Expand DownExpand Up@@ -104,7 +104,8 @@ struct bsrate_summary {
// then error_rate is given a value of 0.
double error_rate{};

void update_pos(const char nt) {
void
update_pos(const char nt) {
if (nt == 'C' || nt == 'T') {
++total_count_positive;
converted_count_positive += (nt == 'T');
Expand All@@ -113,7 +114,8 @@ struct bsrate_summary {
++error_count;
}

void update_neg(const char nt) {
void
update_neg(const char nt) {
if (nt == 'C' || nt == 'T') {
++total_count_negative;
converted_count_negative += (nt == 'T');
Expand All@@ -122,7 +124,8 @@ struct bsrate_summary {
++error_count;
}

bsrate_summary &operator+=(const bsrate_summary &rhs) {
bsrate_summary &
operator+=(const bsrate_summary &rhs) {
// ADS: the "rates" are set to 0.0 here to ensure that they are
// computed properly using the full data after any accumulation of
// integer values has completed.
Expand All@@ -144,7 +147,8 @@ struct bsrate_summary {
return *this;
}

void set_values() {
void
set_values() {
bisulfite_conversion_rate_positive =
static_cast<double>(converted_count_positive) /
max(total_count_positive, static_cast<uint64_t>(1));
Expand All@@ -156,17 +160,17 @@ struct bsrate_summary {
converted_count = converted_count_positive + converted_count_negative;
total_count = total_count_positive + total_count_negative;

bisulfite_conversion_rate =
static_cast<double>(converted_count) /
max(total_count, static_cast<uint64_t>(1));
bisulfite_conversion_rate = static_cast<double>(converted_count) /
max(total_count, static_cast<uint64_t>(1));

valid_count = total_count + error_count;

error_rate = static_cast<double>(error_count) /
max(valid_count, static_cast<uint64_t>(1));
max(valid_count, static_cast<uint64_t>(1));
}

string tostring_as_row() const {
string
tostring_as_row() const {
static constexpr auto precision_val = 5u;
std::ostringstream oss;
oss.precision(precision_val);
Expand All@@ -188,7 +192,32 @@ struct bsrate_summary {
return oss.str();
}

string tostring() const {
string
tostring_as_yaml_list(const uint32_t position) const {
static constexpr auto precision_val = 5u;
std::ostringstream oss;
oss.precision(precision_val);
oss.setf(std::ios_base::fixed, std::ios_base::floatfield);
// clang-format off
oss << " - base: " << position << '\n'
<< " ptot: " << total_count_positive << '\n'
<< " pconv: " << converted_count_positive << '\n'
<< " prate: " << bisulfite_conversion_rate_positive << '\n'
<< " ntot: " << total_count_negative << '\n'
<< " nconv: " << converted_count_negative << '\n'
<< " nrate: " << bisulfite_conversion_rate_negative << '\n'
<< " bthtot: " << total_count << '\n'
<< " bthconv: " << converted_count << '\n'
<< " bthrate: " << bisulfite_conversion_rate << '\n'
<< " err: " << error_count << '\n'
<< " all: " << valid_count << '\n'
<< " errrate: " << error_rate << '\n';
// clang-format on
return oss.str();
}

string
tostring() const {
static constexpr auto sep = ": ";
std::ostringstream oss;
oss << "converted_count_positive" << sep << converted_count_positive
Expand DownExpand Up@@ -357,6 +386,35 @@ write_output(const string &outfile, const vector<bsrate_summary> &summaries) {
out << (i + 1) << '\t' << summaries[i].tostring_as_row() << '\n';
}

static void
write_output_yaml(const string &outfile,
const vector<bsrate_summary> &summaries) {
std::ofstream of;
if (!outfile.empty()) of.open(outfile.c_str());
std::ostream out(outfile.empty() ? std::cout.rdbuf() : of.rdbuf());
if (!out) throw dnmt_error("failed to open output file");

bsrate_summary overall_summary = reduce(cbegin(summaries), cend(summaries));
overall_summary.set_values();
out << "overall_conversion_rate: "
<< overall_summary.bisulfite_conversion_rate << '\n'
<< "pos_conversion_rate: "
<< overall_summary.bisulfite_conversion_rate_positive << '\n'
<< "pos_count: " << overall_summary.total_count_positive << '\n'
<< "neg_conversion_rate: "
<< overall_summary.bisulfite_conversion_rate_negative << '\n'
<< "neg_count: " << overall_summary.total_count_negative << '\n';

// figure out how many positions to print in the output, capped at 1000
auto output_len = std::min(std::size(summaries), 1000ul);
while (output_len > 0 && summaries[output_len - 1].total_count == 0)
--output_len;

out << "rows:\n";
for (auto i = 0u; i < output_len; ++i)
out << summaries[i].tostring_as_yaml_list(i + 1);
}

static void
write_summary(const string &summary_file, vector<bsrate_summary> &summaries) {
auto s = reduce(cbegin(summaries), cend(summaries));
Expand DownExpand Up@@ -422,6 +480,7 @@ main_bsrate(int argc, const char **argv) {

bool VERBOSE = false;
bool INCLUDE_CPGS = false;
bool output_yaml = false;
bool reads_are_a_rich = false;
bool report_per_read = false;
size_t n_threads = 1;
Expand DownExpand Up@@ -453,6 +512,7 @@ main_bsrate(int argc, const char **argv) {
opt_parse.add_opt("bins", 'b', "number of bins for per-read", false,
n_hist_bins);
opt_parse.add_opt("summary", 'S', "summary file name", false, summary_file);
opt_parse.add_opt("yaml", 'y', "output in yaml format", false, output_yaml);
opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
vector<string> leftover_args;
Expand DownExpand Up@@ -563,7 +623,10 @@ main_bsrate(int argc, const char **argv) {
for_each(begin(summaries), end(summaries),
[](bsrate_summary &s) { s.set_values(); });

write_output(outfile, summaries);
if (output_yaml)
write_output_yaml(outfile, summaries);
else
write_output(outfile, summaries);

if (hanging > 0) write_hanging_read_message(cerr, hanging);

Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Yaml output for bsrate#237

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to your account

 Merged

andrewdavidsmith
merged 1 commit into

from

Jun 27, 2024
 Merged


Yaml output for bsrate
#237
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97 changes: 80 additions & 17 deletions
src/analysis/bsrate.cpp

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,12 @@
 * General Public License for more details.
 */

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

#include <bamxx.hpp>

#include <algorithm>
Expand All@@ -28,12 +34,6 @@
#include <unordered_set>
#include <vector>

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

using std::accumulate;
using std::cerr;
using std::cout;
Expand DownExpand Up@@ -104,7 +104,8 @@ struct bsrate_summary {
 // then error_rate is given a value of 0.
 double error_rate{};

 void update_pos(const char nt) {
 void
 update_pos(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_positive;
 converted_count_positive += (nt == 'T');
Expand All@@ -113,7 +114,8 @@ struct bsrate_summary {
 ++error_count;
 }

 void update_neg(const char nt) {
 void
 update_neg(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_negative;
 converted_count_negative += (nt == 'T');
Expand All@@ -122,7 +124,8 @@ struct bsrate_summary {
 ++error_count;
 }

 bsrate_summary &operator+=(const bsrate_summary &rhs) {
 bsrate_summary &
 operator+=(const bsrate_summary &rhs) {
 // ADS: the "rates" are set to 0.0 here to ensure that they are
 // computed properly using the full data after any accumulation of
 // integer values has completed.
Expand All@@ -144,7 +147,8 @@ struct bsrate_summary {
 return *this;
 }

 void set_values() {
 void
 set_values() {
 bisulfite_conversion_rate_positive =
 static_cast<double>(converted_count_positive) /
 max(total_count_positive, static_cast<uint64_t>(1));
Expand All@@ -156,17 +160,17 @@ struct bsrate_summary {
 converted_count = converted_count_positive + converted_count_negative;
 total_count = total_count_positive + total_count_negative;

 bisulfite_conversion_rate =
 static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));
 bisulfite_conversion_rate = static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));

 valid_count = total_count + error_count;

 error_rate = static_cast<double>(error_count) /
 max(valid_count, static_cast<uint64_t>(1));
max(valid_count, static_cast<uint64_t>(1));
 }

 string tostring_as_row() const {
 string
 tostring_as_row() const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
Expand All@@ -188,7 +192,32 @@ struct bsrate_summary {
 return oss.str();
 }

 string tostring() const {
 string
 tostring_as_yaml_list(const uint32_t position) const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
 oss.setf(std::ios_base::fixed, std::ios_base::floatfield);
 // clang-format off
 oss << " - base: " << position << '\n'
 << " ptot: " << total_count_positive << '\n'
 << " pconv: " << converted_count_positive << '\n'
 << " prate: " << bisulfite_conversion_rate_positive << '\n'
 << " ntot: " << total_count_negative << '\n'
 << " nconv: " << converted_count_negative << '\n'
 << " nrate: " << bisulfite_conversion_rate_negative << '\n'
 << " bthtot: " << total_count << '\n'
 << " bthconv: " << converted_count << '\n'
 << " bthrate: " << bisulfite_conversion_rate << '\n'
 << " err: " << error_count << '\n'
 << " all: " << valid_count << '\n'
 << " errrate: " << error_rate << '\n';
 // clang-format on
 return oss.str();
 }

 string
 tostring() const {
 static constexpr auto sep = ": ";
 std::ostringstream oss;
 oss << "converted_count_positive" << sep << converted_count_positive
Expand DownExpand Up@@ -357,6 +386,35 @@ write_output(const string &outfile, const vector<bsrate_summary> &summaries) {
 out << (i + 1) << '\t' << summaries[i].tostring_as_row() << '\n';
}

static void
write_output_yaml(const string &outfile,
 const vector<bsrate_summary> &summaries) {
 std::ofstream of;
 if (!outfile.empty()) of.open(outfile.c_str());
 std::ostream out(outfile.empty() ? std::cout.rdbuf() : of.rdbuf());
 if (!out) throw dnmt_error("failed to open output file");

 bsrate_summary overall_summary = reduce(cbegin(summaries), cend(summaries));
 overall_summary.set_values();
 out << "overall_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate << '\n'
 << "pos_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_positive << '\n'
 << "pos_count: " << overall_summary.total_count_positive << '\n'
 << "neg_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_negative << '\n'
 << "neg_count: " << overall_summary.total_count_negative << '\n';

 // figure out how many positions to print in the output, capped at 1000
 auto output_len = std::min(std::size(summaries), 1000ul);
 while (output_len > 0 && summaries[output_len - 1].total_count == 0)
 --output_len;

 out << "rows:\n";
 for (auto i = 0u; i < output_len; ++i)
 out << summaries[i].tostring_as_yaml_list(i + 1);
}

static void
write_summary(const string &summary_file, vector<bsrate_summary> &summaries) {
 auto s = reduce(cbegin(summaries), cend(summaries));
Expand DownExpand Up@@ -422,6 +480,7 @@ main_bsrate(int argc, const char **argv) {

 bool VERBOSE = false;
 bool INCLUDE_CPGS = false;
 bool output_yaml = false;
 bool reads_are_a_rich = false;
 bool report_per_read = false;
 size_t n_threads = 1;
Expand DownExpand Up@@ -453,6 +512,7 @@ main_bsrate(int argc, const char **argv) {
 opt_parse.add_opt("bins", 'b', "number of bins for per-read", false,
 n_hist_bins);
 opt_parse.add_opt("summary", 'S', "summary file name", false, summary_file);
 opt_parse.add_opt("yaml", 'y', "output in yaml format", false, output_yaml);
 opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
 opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
 vector<string> leftover_args;
Expand DownExpand Up@@ -563,7 +623,10 @@ main_bsrate(int argc, const char **argv) {
 for_each(begin(summaries), end(summaries),
 [](bsrate_summary &s) { s.set_values(); });

 write_output(outfile, summaries);
 if (output_yaml)
 write_output_yaml(outfile, summaries);
 else
 write_output(outfile, summaries);

 if (hanging > 0) write_hanging_read_message(cerr, hanging);

Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Yaml output for bsrate#237

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privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
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to your account

 Merged

andrewdavidsmith
merged 1 commit into

from

Jun 27, 2024
 Merged


Yaml output for bsrate
#237
 Changes from all commits
Commits

Show all changes


1 commit


Select commit


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97 changes: 80 additions & 17 deletions
src/analysis/bsrate.cpp

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,12 @@
 * General Public License for more details.
 */

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

#include <bamxx.hpp>

#include <algorithm>
Expand All@@ -28,12 +34,6 @@
#include <unordered_set>
#include <vector>

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

using std::accumulate;
using std::cerr;
using std::cout;
Expand DownExpand Up@@ -104,7 +104,8 @@ struct bsrate_summary {
 // then error_rate is given a value of 0.
 double error_rate{};

 void update_pos(const char nt) {
 void
 update_pos(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_positive;
 converted_count_positive += (nt == 'T');
Expand All@@ -113,7 +114,8 @@ struct bsrate_summary {
 ++error_count;
 }

 void update_neg(const char nt) {
 void
 update_neg(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_negative;
 converted_count_negative += (nt == 'T');
Expand All@@ -122,7 +124,8 @@ struct bsrate_summary {
 ++error_count;
 }

 bsrate_summary &operator+=(const bsrate_summary &rhs) {
 bsrate_summary &
 operator+=(const bsrate_summary &rhs) {
 // ADS: the "rates" are set to 0.0 here to ensure that they are
 // computed properly using the full data after any accumulation of
 // integer values has completed.
Expand All@@ -144,7 +147,8 @@ struct bsrate_summary {
 return *this;
 }

 void set_values() {
 void
 set_values() {
 bisulfite_conversion_rate_positive =
 static_cast<double>(converted_count_positive) /
 max(total_count_positive, static_cast<uint64_t>(1));
Expand All@@ -156,17 +160,17 @@ struct bsrate_summary {
 converted_count = converted_count_positive + converted_count_negative;
 total_count = total_count_positive + total_count_negative;

 bisulfite_conversion_rate =
 static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));
 bisulfite_conversion_rate = static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));

 valid_count = total_count + error_count;

 error_rate = static_cast<double>(error_count) /
 max(valid_count, static_cast<uint64_t>(1));
max(valid_count, static_cast<uint64_t>(1));
 }

 string tostring_as_row() const {
 string
 tostring_as_row() const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
Expand All@@ -188,7 +192,32 @@ struct bsrate_summary {
 return oss.str();
 }

 string tostring() const {
 string
 tostring_as_yaml_list(const uint32_t position) const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
 oss.setf(std::ios_base::fixed, std::ios_base::floatfield);
 // clang-format off
 oss << " - base: " << position << '\n'
 << " ptot: " << total_count_positive << '\n'
 << " pconv: " << converted_count_positive << '\n'
 << " prate: " << bisulfite_conversion_rate_positive << '\n'
 << " ntot: " << total_count_negative << '\n'
 << " nconv: " << converted_count_negative << '\n'
 << " nrate: " << bisulfite_conversion_rate_negative << '\n'
 << " bthtot: " << total_count << '\n'
 << " bthconv: " << converted_count << '\n'
 << " bthrate: " << bisulfite_conversion_rate << '\n'
 << " err: " << error_count << '\n'
 << " all: " << valid_count << '\n'
 << " errrate: " << error_rate << '\n';
 // clang-format on
 return oss.str();
 }

 string
 tostring() const {
 static constexpr auto sep = ": ";
 std::ostringstream oss;
 oss << "converted_count_positive" << sep << converted_count_positive
Expand DownExpand Up@@ -357,6 +386,35 @@ write_output(const string &outfile, const vector<bsrate_summary> &summaries) {
 out << (i + 1) << '\t' << summaries[i].tostring_as_row() << '\n';
}

static void
write_output_yaml(const string &outfile,
 const vector<bsrate_summary> &summaries) {
 std::ofstream of;
 if (!outfile.empty()) of.open(outfile.c_str());
 std::ostream out(outfile.empty() ? std::cout.rdbuf() : of.rdbuf());
 if (!out) throw dnmt_error("failed to open output file");

 bsrate_summary overall_summary = reduce(cbegin(summaries), cend(summaries));
 overall_summary.set_values();
 out << "overall_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate << '\n'
 << "pos_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_positive << '\n'
 << "pos_count: " << overall_summary.total_count_positive << '\n'
 << "neg_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_negative << '\n'
 << "neg_count: " << overall_summary.total_count_negative << '\n';

 // figure out how many positions to print in the output, capped at 1000
 auto output_len = std::min(std::size(summaries), 1000ul);
 while (output_len > 0 && summaries[output_len - 1].total_count == 0)
 --output_len;

 out << "rows:\n";
 for (auto i = 0u; i < output_len; ++i)
 out << summaries[i].tostring_as_yaml_list(i + 1);
}

static void
write_summary(const string &summary_file, vector<bsrate_summary> &summaries) {
 auto s = reduce(cbegin(summaries), cend(summaries));
Expand DownExpand Up@@ -422,6 +480,7 @@ main_bsrate(int argc, const char **argv) {

 bool VERBOSE = false;
 bool INCLUDE_CPGS = false;
 bool output_yaml = false;
 bool reads_are_a_rich = false;
 bool report_per_read = false;
 size_t n_threads = 1;
Expand DownExpand Up@@ -453,6 +512,7 @@ main_bsrate(int argc, const char **argv) {
 opt_parse.add_opt("bins", 'b', "number of bins for per-read", false,
 n_hist_bins);
 opt_parse.add_opt("summary", 'S', "summary file name", false, summary_file);
 opt_parse.add_opt("yaml", 'y', "output in yaml format", false, output_yaml);
 opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
 opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
 vector<string> leftover_args;
Expand DownExpand Up@@ -563,7 +623,10 @@ main_bsrate(int argc, const char **argv) {
 for_each(begin(summaries), end(summaries),
 [](bsrate_summary &s) { s.set_values(); });

 write_output(outfile, summaries);
 if (output_yaml)
 write_output_yaml(outfile, summaries);
 else
 write_output(outfile, summaries);

 if (hanging > 0) write_hanging_read_message(cerr, hanging);

Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Yaml output for bsrate#237

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Yaml output for bsrate
#237
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97 changes: 80 additions & 17 deletions
src/analysis/bsrate.cpp

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,12 @@
 * General Public License for more details.
 */

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

#include <bamxx.hpp>

#include <algorithm>
Expand All@@ -28,12 +34,6 @@
#include <unordered_set>
#include <vector>

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

using std::accumulate;
using std::cerr;
using std::cout;
Expand DownExpand Up@@ -104,7 +104,8 @@ struct bsrate_summary {
 // then error_rate is given a value of 0.
 double error_rate{};

 void update_pos(const char nt) {
 void
 update_pos(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_positive;
 converted_count_positive += (nt == 'T');
Expand All@@ -113,7 +114,8 @@ struct bsrate_summary {
 ++error_count;
 }

 void update_neg(const char nt) {
 void
 update_neg(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_negative;
 converted_count_negative += (nt == 'T');
Expand All@@ -122,7 +124,8 @@ struct bsrate_summary {
 ++error_count;
 }

 bsrate_summary &operator+=(const bsrate_summary &rhs) {
 bsrate_summary &
 operator+=(const bsrate_summary &rhs) {
 // ADS: the "rates" are set to 0.0 here to ensure that they are
 // computed properly using the full data after any accumulation of
 // integer values has completed.
Expand All@@ -144,7 +147,8 @@ struct bsrate_summary {
 return *this;
 }

 void set_values() {
 void
 set_values() {
 bisulfite_conversion_rate_positive =
 static_cast<double>(converted_count_positive) /
 max(total_count_positive, static_cast<uint64_t>(1));
Expand All@@ -156,17 +160,17 @@ struct bsrate_summary {
 converted_count = converted_count_positive + converted_count_negative;
 total_count = total_count_positive + total_count_negative;

 bisulfite_conversion_rate =
 static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));
 bisulfite_conversion_rate = static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));

 valid_count = total_count + error_count;

 error_rate = static_cast<double>(error_count) /
 max(valid_count, static_cast<uint64_t>(1));
max(valid_count, static_cast<uint64_t>(1));
 }

 string tostring_as_row() const {
 string
 tostring_as_row() const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
Expand All@@ -188,7 +192,32 @@ struct bsrate_summary {
 return oss.str();
 }

 string tostring() const {
 string
 tostring_as_yaml_list(const uint32_t position) const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
 oss.setf(std::ios_base::fixed, std::ios_base::floatfield);
 // clang-format off
 oss << " - base: " << position << '\n'
 << " ptot: " << total_count_positive << '\n'
 << " pconv: " << converted_count_positive << '\n'
 << " prate: " << bisulfite_conversion_rate_positive << '\n'
 << " ntot: " << total_count_negative << '\n'
 << " nconv: " << converted_count_negative << '\n'
 << " nrate: " << bisulfite_conversion_rate_negative << '\n'
 << " bthtot: " << total_count << '\n'
 << " bthconv: " << converted_count << '\n'
 << " bthrate: " << bisulfite_conversion_rate << '\n'
 << " err: " << error_count << '\n'
 << " all: " << valid_count << '\n'
 << " errrate: " << error_rate << '\n';
 // clang-format on
 return oss.str();
 }

 string
 tostring() const {
 static constexpr auto sep = ": ";
 std::ostringstream oss;
 oss << "converted_count_positive" << sep << converted_count_positive
Expand DownExpand Up@@ -357,6 +386,35 @@ write_output(const string &outfile, const vector<bsrate_summary> &summaries) {
 out << (i + 1) << '\t' << summaries[i].tostring_as_row() << '\n';
}

static void
write_output_yaml(const string &outfile,
 const vector<bsrate_summary> &summaries) {
 std::ofstream of;
 if (!outfile.empty()) of.open(outfile.c_str());
 std::ostream out(outfile.empty() ? std::cout.rdbuf() : of.rdbuf());
 if (!out) throw dnmt_error("failed to open output file");

 bsrate_summary overall_summary = reduce(cbegin(summaries), cend(summaries));
 overall_summary.set_values();
 out << "overall_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate << '\n'
 << "pos_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_positive << '\n'
 << "pos_count: " << overall_summary.total_count_positive << '\n'
 << "neg_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_negative << '\n'
 << "neg_count: " << overall_summary.total_count_negative << '\n';

 // figure out how many positions to print in the output, capped at 1000
 auto output_len = std::min(std::size(summaries), 1000ul);
 while (output_len > 0 && summaries[output_len - 1].total_count == 0)
 --output_len;

 out << "rows:\n";
 for (auto i = 0u; i < output_len; ++i)
 out << summaries[i].tostring_as_yaml_list(i + 1);
}

static void
write_summary(const string &summary_file, vector<bsrate_summary> &summaries) {
 auto s = reduce(cbegin(summaries), cend(summaries));
Expand DownExpand Up@@ -422,6 +480,7 @@ main_bsrate(int argc, const char **argv) {

 bool VERBOSE = false;
 bool INCLUDE_CPGS = false;
 bool output_yaml = false;
 bool reads_are_a_rich = false;
 bool report_per_read = false;
 size_t n_threads = 1;
Expand DownExpand Up@@ -453,6 +512,7 @@ main_bsrate(int argc, const char **argv) {
 opt_parse.add_opt("bins", 'b', "number of bins for per-read", false,
 n_hist_bins);
 opt_parse.add_opt("summary", 'S', "summary file name", false, summary_file);
 opt_parse.add_opt("yaml", 'y', "output in yaml format", false, output_yaml);
 opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
 opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
 vector<string> leftover_args;
Expand DownExpand Up@@ -563,7 +623,10 @@ main_bsrate(int argc, const char **argv) {
 for_each(begin(summaries), end(summaries),
 [](bsrate_summary &s) { s.set_values(); });

 write_output(outfile, summaries);
 if (output_yaml)
 write_output_yaml(outfile, summaries);
 else
 write_output(outfile, summaries);

 if (hanging > 0) write_hanging_read_message(cerr, hanging);

Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Yaml output for bsrate#237

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 Merged

andrewdavidsmith
merged 1 commit into

from

Jun 27, 2024
 Merged


Yaml output for bsrate
#237
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97 changes: 80 additions & 17 deletions
src/analysis/bsrate.cpp

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,12 @@
 * General Public License for more details.
 */

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

#include <bamxx.hpp>

#include <algorithm>
Expand All@@ -28,12 +34,6 @@
#include <unordered_set>
#include <vector>

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

using std::accumulate;
using std::cerr;
using std::cout;
Expand DownExpand Up@@ -104,7 +104,8 @@ struct bsrate_summary {
 // then error_rate is given a value of 0.
 double error_rate{};

 void update_pos(const char nt) {
 void
 update_pos(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_positive;
 converted_count_positive += (nt == 'T');
Expand All@@ -113,7 +114,8 @@ struct bsrate_summary {
 ++error_count;
 }

 void update_neg(const char nt) {
 void
 update_neg(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_negative;
 converted_count_negative += (nt == 'T');
Expand All@@ -122,7 +124,8 @@ struct bsrate_summary {
 ++error_count;
 }

 bsrate_summary &operator+=(const bsrate_summary &rhs) {
 bsrate_summary &
 operator+=(const bsrate_summary &rhs) {
 // ADS: the "rates" are set to 0.0 here to ensure that they are
 // computed properly using the full data after any accumulation of
 // integer values has completed.
Expand All@@ -144,7 +147,8 @@ struct bsrate_summary {
 return *this;
 }

 void set_values() {
 void
 set_values() {
 bisulfite_conversion_rate_positive =
 static_cast<double>(converted_count_positive) /
 max(total_count_positive, static_cast<uint64_t>(1));
Expand All@@ -156,17 +160,17 @@ struct bsrate_summary {
 converted_count = converted_count_positive + converted_count_negative;
 total_count = total_count_positive + total_count_negative;

 bisulfite_conversion_rate =
 static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));
 bisulfite_conversion_rate = static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));

 valid_count = total_count + error_count;

 error_rate = static_cast<double>(error_count) /
 max(valid_count, static_cast<uint64_t>(1));
max(valid_count, static_cast<uint64_t>(1));
 }

 string tostring_as_row() const {
 string
 tostring_as_row() const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
Expand All@@ -188,7 +192,32 @@ struct bsrate_summary {
 return oss.str();
 }

 string tostring() const {
 string
 tostring_as_yaml_list(const uint32_t position) const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
 oss.setf(std::ios_base::fixed, std::ios_base::floatfield);
 // clang-format off
 oss << " - base: " << position << '\n'
 << " ptot: " << total_count_positive << '\n'
 << " pconv: " << converted_count_positive << '\n'
 << " prate: " << bisulfite_conversion_rate_positive << '\n'
 << " ntot: " << total_count_negative << '\n'
 << " nconv: " << converted_count_negative << '\n'
 << " nrate: " << bisulfite_conversion_rate_negative << '\n'
 << " bthtot: " << total_count << '\n'
 << " bthconv: " << converted_count << '\n'
 << " bthrate: " << bisulfite_conversion_rate << '\n'
 << " err: " << error_count << '\n'
 << " all: " << valid_count << '\n'
 << " errrate: " << error_rate << '\n';
 // clang-format on
 return oss.str();
 }

 string
 tostring() const {
 static constexpr auto sep = ": ";
 std::ostringstream oss;
 oss << "converted_count_positive" << sep << converted_count_positive
Expand DownExpand Up@@ -357,6 +386,35 @@ write_output(const string &outfile, const vector<bsrate_summary> &summaries) {
 out << (i + 1) << '\t' << summaries[i].tostring_as_row() << '\n';
}

static void
write_output_yaml(const string &outfile,
 const vector<bsrate_summary> &summaries) {
 std::ofstream of;
 if (!outfile.empty()) of.open(outfile.c_str());
 std::ostream out(outfile.empty() ? std::cout.rdbuf() : of.rdbuf());
 if (!out) throw dnmt_error("failed to open output file");

 bsrate_summary overall_summary = reduce(cbegin(summaries), cend(summaries));
 overall_summary.set_values();
 out << "overall_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate << '\n'
 << "pos_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_positive << '\n'
 << "pos_count: " << overall_summary.total_count_positive << '\n'
 << "neg_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_negative << '\n'
 << "neg_count: " << overall_summary.total_count_negative << '\n';

 // figure out how many positions to print in the output, capped at 1000
 auto output_len = std::min(std::size(summaries), 1000ul);
 while (output_len > 0 && summaries[output_len - 1].total_count == 0)
 --output_len;

 out << "rows:\n";
 for (auto i = 0u; i < output_len; ++i)
 out << summaries[i].tostring_as_yaml_list(i + 1);
}

static void
write_summary(const string &summary_file, vector<bsrate_summary> &summaries) {
 auto s = reduce(cbegin(summaries), cend(summaries));
Expand DownExpand Up@@ -422,6 +480,7 @@ main_bsrate(int argc, const char **argv) {

 bool VERBOSE = false;
 bool INCLUDE_CPGS = false;
 bool output_yaml = false;
 bool reads_are_a_rich = false;
 bool report_per_read = false;
 size_t n_threads = 1;
Expand DownExpand Up@@ -453,6 +512,7 @@ main_bsrate(int argc, const char **argv) {
 opt_parse.add_opt("bins", 'b', "number of bins for per-read", false,
 n_hist_bins);
 opt_parse.add_opt("summary", 'S', "summary file name", false, summary_file);
 opt_parse.add_opt("yaml", 'y', "output in yaml format", false, output_yaml);
 opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
 opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
 vector<string> leftover_args;
Expand DownExpand Up@@ -563,7 +623,10 @@ main_bsrate(int argc, const char **argv) {
 for_each(begin(summaries), end(summaries),
 [](bsrate_summary &s) { s.set_values(); });

 write_output(outfile, summaries);
 if (output_yaml)
 write_output_yaml(outfile, summaries);
 else
 write_output(outfile, summaries);

 if (hanging > 0) write_hanging_read_message(cerr, hanging);

Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Yaml output for bsrate#237

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 Merged

andrewdavidsmith
merged 1 commit into

from

Jun 27, 2024
 Merged


Yaml output for bsrate
#237
 Changes from all commits
Commits

Show all changes


1 commit


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97 changes: 80 additions & 17 deletions
src/analysis/bsrate.cpp

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,12 @@
 * General Public License for more details.
 */

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

#include <bamxx.hpp>

#include <algorithm>
Expand All@@ -28,12 +34,6 @@
#include <unordered_set>
#include <vector>

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

using std::accumulate;
using std::cerr;
using std::cout;
Expand DownExpand Up@@ -104,7 +104,8 @@ struct bsrate_summary {
 // then error_rate is given a value of 0.
 double error_rate{};

 void update_pos(const char nt) {
 void
 update_pos(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_positive;
 converted_count_positive += (nt == 'T');
Expand All@@ -113,7 +114,8 @@ struct bsrate_summary {
 ++error_count;
 }

 void update_neg(const char nt) {
 void
 update_neg(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_negative;
 converted_count_negative += (nt == 'T');
Expand All@@ -122,7 +124,8 @@ struct bsrate_summary {
 ++error_count;
 }

 bsrate_summary &operator+=(const bsrate_summary &rhs) {
 bsrate_summary &
 operator+=(const bsrate_summary &rhs) {
 // ADS: the "rates" are set to 0.0 here to ensure that they are
 // computed properly using the full data after any accumulation of
 // integer values has completed.
Expand All@@ -144,7 +147,8 @@ struct bsrate_summary {
 return *this;
 }

 void set_values() {
 void
 set_values() {
 bisulfite_conversion_rate_positive =
 static_cast<double>(converted_count_positive) /
 max(total_count_positive, static_cast<uint64_t>(1));
Expand All@@ -156,17 +160,17 @@ struct bsrate_summary {
 converted_count = converted_count_positive + converted_count_negative;
 total_count = total_count_positive + total_count_negative;

 bisulfite_conversion_rate =
 static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));
 bisulfite_conversion_rate = static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));

 valid_count = total_count + error_count;

 error_rate = static_cast<double>(error_count) /
 max(valid_count, static_cast<uint64_t>(1));
max(valid_count, static_cast<uint64_t>(1));
 }

 string tostring_as_row() const {
 string
 tostring_as_row() const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
Expand All@@ -188,7 +192,32 @@ struct bsrate_summary {
 return oss.str();
 }

 string tostring() const {
 string
 tostring_as_yaml_list(const uint32_t position) const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
 oss.setf(std::ios_base::fixed, std::ios_base::floatfield);
 // clang-format off
 oss << " - base: " << position << '\n'
 << " ptot: " << total_count_positive << '\n'
 << " pconv: " << converted_count_positive << '\n'
 << " prate: " << bisulfite_conversion_rate_positive << '\n'
 << " ntot: " << total_count_negative << '\n'
 << " nconv: " << converted_count_negative << '\n'
 << " nrate: " << bisulfite_conversion_rate_negative << '\n'
 << " bthtot: " << total_count << '\n'
 << " bthconv: " << converted_count << '\n'
 << " bthrate: " << bisulfite_conversion_rate << '\n'
 << " err: " << error_count << '\n'
 << " all: " << valid_count << '\n'
 << " errrate: " << error_rate << '\n';
 // clang-format on
 return oss.str();
 }

 string
 tostring() const {
 static constexpr auto sep = ": ";
 std::ostringstream oss;
 oss << "converted_count_positive" << sep << converted_count_positive
Expand DownExpand Up@@ -357,6 +386,35 @@ write_output(const string &outfile, const vector<bsrate_summary> &summaries) {
 out << (i + 1) << '\t' << summaries[i].tostring_as_row() << '\n';
}

static void
write_output_yaml(const string &outfile,
 const vector<bsrate_summary> &summaries) {
 std::ofstream of;
 if (!outfile.empty()) of.open(outfile.c_str());
 std::ostream out(outfile.empty() ? std::cout.rdbuf() : of.rdbuf());
 if (!out) throw dnmt_error("failed to open output file");

 bsrate_summary overall_summary = reduce(cbegin(summaries), cend(summaries));
 overall_summary.set_values();
 out << "overall_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate << '\n'
 << "pos_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_positive << '\n'
 << "pos_count: " << overall_summary.total_count_positive << '\n'
 << "neg_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_negative << '\n'
 << "neg_count: " << overall_summary.total_count_negative << '\n';

 // figure out how many positions to print in the output, capped at 1000
 auto output_len = std::min(std::size(summaries), 1000ul);
 while (output_len > 0 && summaries[output_len - 1].total_count == 0)
 --output_len;

 out << "rows:\n";
 for (auto i = 0u; i < output_len; ++i)
 out << summaries[i].tostring_as_yaml_list(i + 1);
}

static void
write_summary(const string &summary_file, vector<bsrate_summary> &summaries) {
 auto s = reduce(cbegin(summaries), cend(summaries));
Expand DownExpand Up@@ -422,6 +480,7 @@ main_bsrate(int argc, const char **argv) {

 bool VERBOSE = false;
 bool INCLUDE_CPGS = false;
 bool output_yaml = false;
 bool reads_are_a_rich = false;
 bool report_per_read = false;
 size_t n_threads = 1;
Expand DownExpand Up@@ -453,6 +512,7 @@ main_bsrate(int argc, const char **argv) {
 opt_parse.add_opt("bins", 'b', "number of bins for per-read", false,
 n_hist_bins);
 opt_parse.add_opt("summary", 'S', "summary file name", false, summary_file);
 opt_parse.add_opt("yaml", 'y', "output in yaml format", false, output_yaml);
 opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
 opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
 vector<string> leftover_args;
Expand DownExpand Up@@ -563,7 +623,10 @@ main_bsrate(int argc, const char **argv) {
 for_each(begin(summaries), end(summaries),
 [](bsrate_summary &s) { s.set_values(); });

 write_output(outfile, summaries);
 if (output_yaml)
 write_output_yaml(outfile, summaries);
 else
 write_output(outfile, summaries);

 if (hanging > 0) write_hanging_read_message(cerr, hanging);

Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Yaml output for bsrate#237

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andrewdavidsmith
merged 1 commit into

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Jun 27, 2024
 Merged


Yaml output for bsrate
#237
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97 changes: 80 additions & 17 deletions
src/analysis/bsrate.cpp

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,12 @@
 * General Public License for more details.
 */

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

#include <bamxx.hpp>

#include <algorithm>
Expand All@@ -28,12 +34,6 @@
#include <unordered_set>
#include <vector>

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

using std::accumulate;
using std::cerr;
using std::cout;
Expand DownExpand Up@@ -104,7 +104,8 @@ struct bsrate_summary {
 // then error_rate is given a value of 0.
 double error_rate{};

 void update_pos(const char nt) {
 void
 update_pos(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_positive;
 converted_count_positive += (nt == 'T');
Expand All@@ -113,7 +114,8 @@ struct bsrate_summary {
 ++error_count;
 }

 void update_neg(const char nt) {
 void
 update_neg(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_negative;
 converted_count_negative += (nt == 'T');
Expand All@@ -122,7 +124,8 @@ struct bsrate_summary {
 ++error_count;
 }

 bsrate_summary &operator+=(const bsrate_summary &rhs) {
 bsrate_summary &
 operator+=(const bsrate_summary &rhs) {
 // ADS: the "rates" are set to 0.0 here to ensure that they are
 // computed properly using the full data after any accumulation of
 // integer values has completed.
Expand All@@ -144,7 +147,8 @@ struct bsrate_summary {
 return *this;
 }

 void set_values() {
 void
 set_values() {
 bisulfite_conversion_rate_positive =
 static_cast<double>(converted_count_positive) /
 max(total_count_positive, static_cast<uint64_t>(1));
Expand All@@ -156,17 +160,17 @@ struct bsrate_summary {
 converted_count = converted_count_positive + converted_count_negative;
 total_count = total_count_positive + total_count_negative;

 bisulfite_conversion_rate =
 static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));
 bisulfite_conversion_rate = static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));

 valid_count = total_count + error_count;

 error_rate = static_cast<double>(error_count) /
 max(valid_count, static_cast<uint64_t>(1));
max(valid_count, static_cast<uint64_t>(1));
 }

 string tostring_as_row() const {
 string
 tostring_as_row() const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
Expand All@@ -188,7 +192,32 @@ struct bsrate_summary {
 return oss.str();
 }

 string tostring() const {
 string
 tostring_as_yaml_list(const uint32_t position) const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
 oss.setf(std::ios_base::fixed, std::ios_base::floatfield);
 // clang-format off
 oss << " - base: " << position << '\n'
 << " ptot: " << total_count_positive << '\n'
 << " pconv: " << converted_count_positive << '\n'
 << " prate: " << bisulfite_conversion_rate_positive << '\n'
 << " ntot: " << total_count_negative << '\n'
 << " nconv: " << converted_count_negative << '\n'
 << " nrate: " << bisulfite_conversion_rate_negative << '\n'
 << " bthtot: " << total_count << '\n'
 << " bthconv: " << converted_count << '\n'
 << " bthrate: " << bisulfite_conversion_rate << '\n'
 << " err: " << error_count << '\n'
 << " all: " << valid_count << '\n'
 << " errrate: " << error_rate << '\n';
 // clang-format on
 return oss.str();
 }

 string
 tostring() const {
 static constexpr auto sep = ": ";
 std::ostringstream oss;
 oss << "converted_count_positive" << sep << converted_count_positive
Expand DownExpand Up@@ -357,6 +386,35 @@ write_output(const string &outfile, const vector<bsrate_summary> &summaries) {
 out << (i + 1) << '\t' << summaries[i].tostring_as_row() << '\n';
}

static void
write_output_yaml(const string &outfile,
 const vector<bsrate_summary> &summaries) {
 std::ofstream of;
 if (!outfile.empty()) of.open(outfile.c_str());
 std::ostream out(outfile.empty() ? std::cout.rdbuf() : of.rdbuf());
 if (!out) throw dnmt_error("failed to open output file");

 bsrate_summary overall_summary = reduce(cbegin(summaries), cend(summaries));
 overall_summary.set_values();
 out << "overall_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate << '\n'
 << "pos_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_positive << '\n'
 << "pos_count: " << overall_summary.total_count_positive << '\n'
 << "neg_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_negative << '\n'
 << "neg_count: " << overall_summary.total_count_negative << '\n';

 // figure out how many positions to print in the output, capped at 1000
 auto output_len = std::min(std::size(summaries), 1000ul);
 while (output_len > 0 && summaries[output_len - 1].total_count == 0)
 --output_len;

 out << "rows:\n";
 for (auto i = 0u; i < output_len; ++i)
 out << summaries[i].tostring_as_yaml_list(i + 1);
}

static void
write_summary(const string &summary_file, vector<bsrate_summary> &summaries) {
 auto s = reduce(cbegin(summaries), cend(summaries));
Expand DownExpand Up@@ -422,6 +480,7 @@ main_bsrate(int argc, const char **argv) {

 bool VERBOSE = false;
 bool INCLUDE_CPGS = false;
 bool output_yaml = false;
 bool reads_are_a_rich = false;
 bool report_per_read = false;
 size_t n_threads = 1;
Expand DownExpand Up@@ -453,6 +512,7 @@ main_bsrate(int argc, const char **argv) {
 opt_parse.add_opt("bins", 'b', "number of bins for per-read", false,
 n_hist_bins);
 opt_parse.add_opt("summary", 'S', "summary file name", false, summary_file);
 opt_parse.add_opt("yaml", 'y', "output in yaml format", false, output_yaml);
 opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
 opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
 vector<string> leftover_args;
Expand DownExpand Up@@ -563,7 +623,10 @@ main_bsrate(int argc, const char **argv) {
 for_each(begin(summaries), end(summaries),
 [](bsrate_summary &s) { s.set_values(); });

 write_output(outfile, summaries);
 if (output_yaml)
 write_output_yaml(outfile, summaries);
 else
 write_output(outfile, summaries);

 if (hanging > 0) write_hanging_read_message(cerr, hanging);

Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Yaml output for bsrate#237

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privacy statement. We’ll occasionally send you account related emails.

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 Merged

andrewdavidsmith
merged 1 commit into

from

Jun 27, 2024
 Merged


Yaml output for bsrate
#237
 Changes from all commits
Commits

Show all changes


1 commit


Select commit


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Filter by extension
Filter by extension
Conversations

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97 changes: 80 additions & 17 deletions
src/analysis/bsrate.cpp

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -17,6 +17,12 @@
 * General Public License for more details.
 */

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

#include <bamxx.hpp>

#include <algorithm>
Expand All@@ -28,12 +34,6 @@
#include <unordered_set>
#include <vector>

#include "OptionParser.hpp"
#include "bam_record_utils.hpp"
#include "bsutils.hpp"
#include "dnmt_error.hpp"
#include "smithlab_utils.hpp"

using std::accumulate;
using std::cerr;
using std::cout;
Expand DownExpand Up@@ -104,7 +104,8 @@ struct bsrate_summary {
 // then error_rate is given a value of 0.
 double error_rate{};

 void update_pos(const char nt) {
 void
 update_pos(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_positive;
 converted_count_positive += (nt == 'T');
Expand All@@ -113,7 +114,8 @@ struct bsrate_summary {
 ++error_count;
 }

 void update_neg(const char nt) {
 void
 update_neg(const char nt) {
 if (nt == 'C' || nt == 'T') {
 ++total_count_negative;
 converted_count_negative += (nt == 'T');
Expand All@@ -122,7 +124,8 @@ struct bsrate_summary {
 ++error_count;
 }

 bsrate_summary &operator+=(const bsrate_summary &rhs) {
 bsrate_summary &
 operator+=(const bsrate_summary &rhs) {
 // ADS: the "rates" are set to 0.0 here to ensure that they are
 // computed properly using the full data after any accumulation of
 // integer values has completed.
Expand All@@ -144,7 +147,8 @@ struct bsrate_summary {
 return *this;
 }

 void set_values() {
 void
 set_values() {
 bisulfite_conversion_rate_positive =
 static_cast<double>(converted_count_positive) /
 max(total_count_positive, static_cast<uint64_t>(1));
Expand All@@ -156,17 +160,17 @@ struct bsrate_summary {
 converted_count = converted_count_positive + converted_count_negative;
 total_count = total_count_positive + total_count_negative;

 bisulfite_conversion_rate =
 static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));
 bisulfite_conversion_rate = static_cast<double>(converted_count) /
 max(total_count, static_cast<uint64_t>(1));

 valid_count = total_count + error_count;

 error_rate = static_cast<double>(error_count) /
 max(valid_count, static_cast<uint64_t>(1));
max(valid_count, static_cast<uint64_t>(1));
 }

 string tostring_as_row() const {
 string
 tostring_as_row() const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
Expand All@@ -188,7 +192,32 @@ struct bsrate_summary {
 return oss.str();
 }

 string tostring() const {
 string
 tostring_as_yaml_list(const uint32_t position) const {
 static constexpr auto precision_val = 5u;
 std::ostringstream oss;
 oss.precision(precision_val);
 oss.setf(std::ios_base::fixed, std::ios_base::floatfield);
 // clang-format off
 oss << " - base: " << position << '\n'
 << " ptot: " << total_count_positive << '\n'
 << " pconv: " << converted_count_positive << '\n'
 << " prate: " << bisulfite_conversion_rate_positive << '\n'
 << " ntot: " << total_count_negative << '\n'
 << " nconv: " << converted_count_negative << '\n'
 << " nrate: " << bisulfite_conversion_rate_negative << '\n'
 << " bthtot: " << total_count << '\n'
 << " bthconv: " << converted_count << '\n'
 << " bthrate: " << bisulfite_conversion_rate << '\n'
 << " err: " << error_count << '\n'
 << " all: " << valid_count << '\n'
 << " errrate: " << error_rate << '\n';
 // clang-format on
 return oss.str();
 }

 string
 tostring() const {
 static constexpr auto sep = ": ";
 std::ostringstream oss;
 oss << "converted_count_positive" << sep << converted_count_positive
Expand DownExpand Up@@ -357,6 +386,35 @@ write_output(const string &outfile, const vector<bsrate_summary> &summaries) {
 out << (i + 1) << '\t' << summaries[i].tostring_as_row() << '\n';
}

static void
write_output_yaml(const string &outfile,
 const vector<bsrate_summary> &summaries) {
 std::ofstream of;
 if (!outfile.empty()) of.open(outfile.c_str());
 std::ostream out(outfile.empty() ? std::cout.rdbuf() : of.rdbuf());
 if (!out) throw dnmt_error("failed to open output file");

 bsrate_summary overall_summary = reduce(cbegin(summaries), cend(summaries));
 overall_summary.set_values();
 out << "overall_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate << '\n'
 << "pos_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_positive << '\n'
 << "pos_count: " << overall_summary.total_count_positive << '\n'
 << "neg_conversion_rate: "
 << overall_summary.bisulfite_conversion_rate_negative << '\n'
 << "neg_count: " << overall_summary.total_count_negative << '\n';

 // figure out how many positions to print in the output, capped at 1000
 auto output_len = std::min(std::size(summaries), 1000ul);
 while (output_len > 0 && summaries[output_len - 1].total_count == 0)
 --output_len;

 out << "rows:\n";
 for (auto i = 0u; i < output_len; ++i)
 out << summaries[i].tostring_as_yaml_list(i + 1);
}

static void
write_summary(const string &summary_file, vector<bsrate_summary> &summaries) {
 auto s = reduce(cbegin(summaries), cend(summaries));
Expand DownExpand Up@@ -422,6 +480,7 @@ main_bsrate(int argc, const char **argv) {

 bool VERBOSE = false;
 bool INCLUDE_CPGS = false;
 bool output_yaml = false;
 bool reads_are_a_rich = false;
 bool report_per_read = false;
 size_t n_threads = 1;
Expand DownExpand Up@@ -453,6 +512,7 @@ main_bsrate(int argc, const char **argv) {
 opt_parse.add_opt("bins", 'b', "number of bins for per-read", false,
 n_hist_bins);
 opt_parse.add_opt("summary", 'S', "summary file name", false, summary_file);
 opt_parse.add_opt("yaml", 'y', "output in yaml format", false, output_yaml);
 opt_parse.add_opt("threads", 't', "number of threads", false, n_threads);
 opt_parse.add_opt("verbose", 'v', "print more run info", false, VERBOSE);
 vector<string> leftover_args;
Expand DownExpand Up@@ -563,7 +623,10 @@ main_bsrate(int argc, const char **argv) {
 for_each(begin(summaries), end(summaries),
 [](bsrate_summary &s) { s.set_values(); });

 write_output(outfile, summaries);
 if (output_yaml)
 write_output_yaml(outfile, summaries);
 else
 write_output(outfile, summaries);

 if (hanging > 0) write_hanging_read_message(cerr, hanging);

Expand Down