MikkelSchubert / adapterremoval / #39

Committed 20 Aug 2024 01:31PM UTC coverage: 79.602% (-3.8%) from 83.365%

Build # #39

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MikkelSchubert

Commit Message

update schema URL to use github pages

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/src/strutils.cpp

/*************************************************************************\
 * AdapterRemoval - cleaning next-generation sequencing reads            *
 *                                                                       *
 * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com           *
 *                                                                       *
 * This program is free software: you can redistribute it and/or modify  *
 * it under the terms of the GNU General Public License as published by  *
 * the Free Software Foundation, either version 3 of the License, or     *
 * (at your option) any later version.                                   *
 *                                                                       *
 * This program is distributed in the hope that it will be useful,       *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 * GNU General Public License for more details.                          *
 *                                                                       *
 * You should have received a copy of the GNU General Public License     *
 * along with this program.  If not, see <http://www.gnu.org/licenses/>. *
\*************************************************************************/
#include "strutils.hpp" // declarations
#include "debug.hpp"    // for AR_REQUIRE
#include <algorithm>    // for min, reverse, max
#include <cctype>       // for isprint, isalnum, tolower, toupper
#include <chrono>       // for system_clock
#include <cmath>        // for log10, pow, round
#include <cstdint>      // for uint64_t, int64_t
#include <iomanip>      // for operator<<, setprecision
#include <limits>       // for numeric_limits
#include <sstream>      // for ostringstream, operator<<, basic_ostream, bas...
#include <stdexcept>    // for invalid_argument
#include <unistd.h>     // for STDOUT_FILENO
#include <vector>       // for vector, swap

namespace adapterremoval {

namespace {

string_vec
indent(string_vec lines, size_t n_indent, bool indent_first)
{
  const std::string indentation(n_indent, ' ');
  for (auto it = lines.begin(); it != lines.end(); ++it) {
    if (!it->empty() && (indent_first || it != lines.begin())) {
      it->insert(0, indentation);
    }
  }

  return lines;
}

} // namespace

size_t
levenshtein(const std::string_view s, const std::string_view t)
{
  std::vector<size_t> v0(t.size() + 1, 0);
  std::vector<size_t> v1(t.size() + 1, 0);

  for (size_t i = 0; i < v0.size(); ++i) {
    v0.at(i) = i;
  }

  for (size_t i = 0; i < s.size(); ++i) {
    v1.at(0) = i + 1;

    for (size_t j = 0; j < t.size(); ++j) {
      const auto del = v0.at(j + 1) + 1;
      const auto ins = v1.at(j) + 1;
      const auto sub = s.at(i) == t.at(j) ? v0.at(j) : v0.at(j) + 1;

      v1.at(j + 1) = std::min(del, std::min(ins, sub));
    }

    std::swap(v0, v1);
  }

  return v0.back();
}

std::string
timestamp(const char* format, const bool milliseconds)
{
  AR_REQUIRE(format);
  using namespace std::chrono;

  const auto now = system_clock::now();
  const auto in_time_t = system_clock::to_time_t(now);

  tm in_localtime{};
  std::ostringstream ss;
  ss << std::put_time(localtime_r(&in_time_t, &in_localtime), format);

  if (milliseconds) {
    const auto ms =
      duration_cast<std::chrono::milliseconds>(now.time_since_epoch());
    ss << '.' << std::setfill('0') << std::setw(3) << (ms.count() % 1000);
  }

  return ss.str();
}

unsigned
str_to_unsigned(const std::string& s)
{
  std::istringstream stream(s);
  int64_t temp = 0;

  if (!(stream >> temp)) {
    throw std::invalid_argument("value is not a valid number");
  }

  // Failing on trailing, non-numerical values
  std::string trailing;
  if (stream >> trailing) {
    throw std::invalid_argument("value contains trailing text");
  }

  if (temp < 0 || temp > std::numeric_limits<unsigned>::max()) {
    throw std::invalid_argument("numerical value overflows");
  }

  return static_cast<unsigned>(temp);
}

std::string
to_lower(std::string str)
{
  for (auto& current : str) {
    current = to_lower(current);
  }

  return str;
}

std::string
to_upper(std::string str)
{
  for (auto& current : str) {
    current = to_upper(current);
  }

  return str;
}

bool
starts_with(const std::string_view str1, const std::string_view str2)
{
  if (str1.size() < str2.size()) {
    return false;
  }

  return str1.substr(0, str2.size()) == str2;
}

bool
ends_with(const std::string_view str1, const std::string_view str2)
{
  if (str1.size() < str2.size()) {
    return false;
  }

  return str1.substr(str1.size() - str2.size()) == str2;
}

string_vec
split_text(const std::string_view text, const char separator)
{
  string_vec lines;

  size_t start = 0;
  size_t end = std::string::npos;
  do {
    end = text.find(separator, start);

    lines.push_back(std::string{ text.substr(start, end - start) });

    start = end + 1;
  } while (end != std::string::npos);

  return lines;
}

std::string
indent_lines(const std::string_view lines, size_t indentation)
{
  return join_text(indent(split_lines(lines), indentation, true), "\n");
}

string_vec
wrap_text(const std::string& value, size_t max_width, size_t ljust)
{
  size_t current_width = 0;
  size_t current_ljust = 0;
  std::istringstream lines_in(value);
  string_vec lines_out;

  std::string substr;
  while (lines_in >> substr) {
    if (current_width) {
      if (current_ljust + current_width + 1 + substr.length() > max_width) {
        current_ljust = ljust;
        lines_out.emplace_back(current_ljust, ' ');
        lines_out.back().append(substr);
        current_width = substr.length();
      } else {
        lines_out.back().push_back(' ');
        lines_out.back().append(substr);
        current_width += substr.length() + 1;
      }
    } else {
      lines_out.push_back(substr);
      current_width += substr.length();
    }
  }

  return lines_out;
}

///////////////////////////////////////////////////////////////////////////////
// Implementations for 'cli_formatter'

cli_formatter::cli_formatter()
  : m_indent_first(true)
  , m_ljust(0)
  , m_columns(DEFAULT_MAX_COLUMNS)
  , m_indentation(4)
{
}

cli_formatter&
cli_formatter::set_column_width(size_t value)
{
  m_columns = value;

  return *this;
}

cli_formatter&
cli_formatter::set_ljust(size_t value)
{
  m_ljust = value;

  return *this;
}

cli_formatter&
cli_formatter::set_indent(size_t value)
{
  m_indentation = value;

  return *this;
}

cli_formatter&
cli_formatter::set_indent_first_line(bool value)
{
  m_indent_first = value;

  return *this;
}

std::string
cli_formatter::format(const std::string_view value) const
{
  std::ostringstream lines_out;

  for (const auto& line : split_lines(value)) {
    const auto block = wrap_text(line, m_columns, m_ljust);

    lines_out << join_text(indent(block, m_indentation, m_indent_first), "\n");
  }

  return lines_out.str();
}

std::string
shell_escape(const std::string_view s)
{
  if (s.empty()) {
    return "''";
  }

  for (const auto c : s) {
    // Conservative list of safe values; better safe than sorry
    if (!isalnum(c) && c != '_' && c != '.' && c != '/' && c != '-') {
      return log_escape(s);
    }
  }

  return std::string{ s };
}

std::string
log_escape(const std::string_view s)
{
  std::string out;
  out.push_back('\'');

  for (const auto c : s) {
    switch (c) {
      case '\'':
        out.append("\\'");
        break;
      case '\\':
        out.append("\\\\");
        break;
      case '\b':
        out.append("\\b");
        break;
      case '\f':
        out.append("\\f");
        break;
      case '\n':
        out.append("\\n");
        break;
      case '\r':
        out.append("\\r");
        break;
      case '\t':
        out.append("\\t");
        break;
      default:
        if (!std::isprint(c)) {
          std::ostringstream ss;
          ss << "\\x" << std::hex << static_cast<int>(c);

          out.append(ss.str());

        } else {
          out.push_back(c);
        }
    }
  }

  out.push_back('\'');

  return out;
}

std::string
shell_escape_command(const string_vec& values)
{
  std::ostringstream ss;
  for (size_t i = 0; i < values.size(); ++i) {
    if (i) {
      ss << ' ';
    }

    ss << shell_escape(values.at(i));
  }

  return ss.str();
}

std::string
format_thousand_sep(size_t count)
{
  if (!count) {
    return "0";
  }

  std::string ss;
  for (size_t i = 0; count; ++i) {
    ss.push_back('0' + (count % 10));
    count /= 10;
    if (count && i && i % 3 == 2) {
      ss.push_back(',');
    }
  }

  std::reverse(ss.begin(), ss.end());

  return ss;
}

std::string
format_rough_number(size_t value, size_t out_digits)
{
  AR_REQUIRE(out_digits > 0);
  if (value == 0) {
    return "0";
  }

  auto rounded = static_cast<double>(value);
  auto in_digits = static_cast<size_t>(std::log10(rounded));
  if (out_digits > in_digits) {
    return std::to_string(value);
  }

  // Round to desired number of significant digits
  const auto tmp = std::pow(10, in_digits - out_digits + 1);
  rounded = std::round(rounded / tmp) * tmp;

  // Rounding up may result in the number of digits increasing
  in_digits = static_cast<size_t>(std::log10(rounded));

  const std::string units = "KMGTP";
  const size_t unit = std::min<size_t>(units.size(), in_digits / 3);
  const double scaled = rounded / std::pow(10.0, unit * 3);
  const size_t precision =
    out_digits - std::min<size_t>(out_digits, in_digits - unit * 3 + 1);

  std::ostringstream ss;
  ss << std::fixed << std::setprecision(precision) << scaled;

  if (unit) {
    ss << " " << units.at(unit - 1);
  }

  return ss.str();
}

std::string
format_fraction(uint64_t num, uint64_t denom, size_t precision)
{
  if (denom) {
    const double fraction = static_cast<double>(num) / denom;

    std::ostringstream ss;
    ss << std::fixed << std::setprecision(precision) << fraction;

    return ss.str();
  } else {
    return "NA";
  }
}

std::string
format_percentage(uint64_t num, uint64_t denom, size_t precision)
{
  return format_fraction(num * 100, denom, precision);
}

} // namespace adapterremoval

1	/*************************************************************************\
2	* AdapterRemoval - cleaning next-generation sequencing reads *
3	* *
4	* Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com *
5	* *
6	* This program is free software: you can redistribute it and/or modify *
7	* it under the terms of the GNU General Public License as published by *
8	* the Free Software Foundation, either version 3 of the License, or *
9	* (at your option) any later version. *
10	* *
11	* This program is distributed in the hope that it will be useful, *
12	* but WITHOUT ANY WARRANTY; without even the implied warranty of *
13	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
14	* GNU General Public License for more details. *
15	* *
16	* You should have received a copy of the GNU General Public License *
17	* along with this program. If not, see <http://www.gnu.org/licenses/>. *
18	\*************************************************************************/
19	#include "strutils.hpp" // declarations
20	#include "debug.hpp" // for AR_REQUIRE
21	#include <algorithm> // for min, reverse, max
22	#include <cctype> // for isprint, isalnum, tolower, toupper
23	#include <chrono> // for system_clock
24	#include <cmath> // for log10, pow, round
25	#include <cstdint> // for uint64_t, int64_t
26	#include <iomanip> // for operator<<, setprecision
27	#include <limits> // for numeric_limits
28	#include <sstream> // for ostringstream, operator<<, basic_ostream, bas...
29	#include <stdexcept> // for invalid_argument
30	#include <unistd.h> // for STDOUT_FILENO
31	#include <vector> // for vector, swap
32
33	namespace adapterremoval {
34
35	namespace {
36
37	string_vec
38	indent(string_vec lines, size_t n_indent, bool indent_first)	91✔
39	{
40	const std::string indentation(n_indent, ' ');	182✔
41	for (auto it = lines.begin(); it != lines.end(); ++it) {	715✔
42	if (!it->empty() && (indent_first \|\| it != lines.begin())) {	348✔
43	it->insert(0, indentation);	167✔
44	}
45	}
46
47	return lines;	273✔
48	}	91✔
49
50	} // namespace
51
52	size_t
53	levenshtein(const std::string_view s, const std::string_view t)	17✔
54	{
55	std::vector<size_t> v0(t.size() + 1, 0);	17✔
56	std::vector<size_t> v1(t.size() + 1, 0);	17✔
57
58	for (size_t i = 0; i < v0.size(); ++i) {	156✔
59	v0.at(i) = i;	122✔
60	}
61
62	for (size_t i = 0; i < s.size(); ++i) {	58✔
63	v1.at(0) = i + 1;	82✔
64
65	for (size_t j = 0; j < t.size(); ++j) {	214✔
66	const auto del = v0.at(j + 1) + 1;	346✔
67	const auto ins = v1.at(j) + 1;	346✔
68	const auto sub = s.at(i) == t.at(j) ? v0.at(j) : v0.at(j) + 1;	692✔
69
70	v1.at(j + 1) = std::min(del, std::min(ins, sub));	692✔
71	}
72
73	std::swap(v0, v1);	82✔
74	}
75
76	return v0.back();	51✔
77	}	34✔
78
79	std::string
80	timestamp(const char* format, const bool milliseconds)	3✔
81	{
82	AR_REQUIRE(format);	3✔
83	using namespace std::chrono;	3✔
84
85	const auto now = system_clock::now();	3✔
86	const auto in_time_t = system_clock::to_time_t(now);	3✔
87
88	tm in_localtime{};	3✔
89	std::ostringstream ss;	3✔
90	ss << std::put_time(localtime_r(&in_time_t, &in_localtime), format);	3✔
91
92	if (milliseconds) {	3✔
93	const auto ms =	3✔
94	duration_cast<std::chrono::milliseconds>(now.time_since_epoch());	6✔
95	ss << '.' << std::setfill('0') << std::setw(3) << (ms.count() % 1000);	12✔
96	}
97
98	return ss.str();	6✔
99	}	3✔
100
101	unsigned
102	str_to_unsigned(const std::string& s)	38✔
103	{
104	std::istringstream stream(s);	38✔
105	int64_t temp = 0;	38✔
106
107	if (!(stream >> temp)) {	114✔
108	throw std::invalid_argument("value is not a valid number");	8✔
109	}
110
111	// Failing on trailing, non-numerical values
112	std::string trailing;	30✔
113	if (stream >> trailing) {	60✔
114	throw std::invalid_argument("value contains trailing text");	4✔
115	}
116
117	if (temp < 0 \|\| temp > std::numeric_limits<unsigned>::max()) {	26✔
118	throw std::invalid_argument("numerical value overflows");	6✔
119	}
120
121	return static_cast<unsigned>(temp);	40✔
122	}	38✔
123
124	std::string
125	to_lower(std::string str)	14✔
126	{
127	for (auto& current : str) {	200✔
128	current = to_lower(current);	56✔
129	}
130
131	return str;	14✔
132	}
133
134	std::string
135	to_upper(std::string str)	2✔
136	{
137	for (auto& current : str) {	44✔
138	current = to_upper(current);	16✔
139	}
140
141	return str;	2✔
142	}
143
144	bool
145	starts_with(const std::string_view str1, const std::string_view str2)	19✔
146	{
147	if (str1.size() < str2.size()) {	19✔
148	return false;
149	}
150
151	return str1.substr(0, str2.size()) == str2;	17✔
152	}
153
154	bool
155	ends_with(const std::string_view str1, const std::string_view str2)	13✔
156	{
157	if (str1.size() < str2.size()) {	13✔
158	return false;
159	}
160
161	return str1.substr(str1.size() - str2.size()) == str2;	11✔
162	}
163
164	string_vec
165	split_text(const std::string_view text, const char separator)	180✔
166	{
167	string_vec lines;	180✔
168
169	size_t start = 0;	180✔
170	size_t end = std::string::npos;	180✔
171	do {	216✔
172	end = text.find(separator, start);	216✔
173
174	lines.push_back(std::string{ text.substr(start, end - start) });	648✔
175
176	start = end + 1;	216✔
177	} while (end != std::string::npos);	216✔
178
179	return lines;	180✔
180	}	×
181
182	std::string
183	indent_lines(const std::string_view lines, size_t indentation)	11✔
184	{
185	return join_text(indent(split_lines(lines), indentation, true), "\n");	44✔
186	}
187
188	string_vec
189	wrap_text(const std::string& value, size_t max_width, size_t ljust)	115✔
190	{
191	size_t current_width = 0;	115✔
192	size_t current_ljust = 0;	115✔
193	std::istringstream lines_in(value);	115✔
194	string_vec lines_out;	115✔
195
196	std::string substr;	115✔
197	while (lines_in >> substr) {	1,120✔
198	if (current_width) {	445✔
199	if (current_ljust + current_width + 1 + substr.length() > max_width) {	676✔
200	current_ljust = ljust;	28✔
201	lines_out.emplace_back(current_ljust, ' ');	28✔
202	lines_out.back().append(substr);	56✔
203	current_width = substr.length();	56✔
204	} else {
205	lines_out.back().push_back(' ');	620✔
206	lines_out.back().append(substr);	620✔
207	current_width += substr.length() + 1;	620✔
208	}
209	} else {
210	lines_out.push_back(substr);	107✔
211	current_width += substr.length();	214✔
212	}
213	}
214
215	return lines_out;	230✔
216	}	115✔
217
218	///////////////////////////////////////////////////////////////////////////////
219	// Implementations for 'cli_formatter'
220
221	cli_formatter::cli_formatter()	50✔
222	: m_indent_first(true)	50✔
223	, m_ljust(0)	50✔
224	, m_columns(DEFAULT_MAX_COLUMNS)	50✔
225	, m_indentation(4)	50✔
226	{
227	}	50✔
228
229	cli_formatter&
230	cli_formatter::set_column_width(size_t value)	50✔
231	{
232	m_columns = value;	50✔
233
234	return *this;	50✔
235	}
236
237	cli_formatter&
238	cli_formatter::set_ljust(size_t value)	32✔
239	{
240	m_ljust = value;	32✔
241
242	return *this;	32✔
243	}
244
245	cli_formatter&
246	cli_formatter::set_indent(size_t value)	50✔
247	{
248	m_indentation = value;	50✔
249
250	return *this;	50✔
251	}
252
253	cli_formatter&
254	cli_formatter::set_indent_first_line(bool value)	18✔
255	{
256	m_indent_first = value;	18✔
257
258	return *this;	18✔
259	}
260
261	std::string
262	cli_formatter::format(const std::string_view value) const	80✔
263	{
264	std::ostringstream lines_out;	80✔
265
266	for (const auto& line : split_lines(value)) {	720✔
267	const auto block = wrap_text(line, m_columns, m_ljust);	80✔
268
269	lines_out << join_text(indent(block, m_indentation, m_indent_first), "\n");	400✔
270	}	160✔
271
272	return lines_out.str();	160✔
273	}	80✔
274
275	std::string
276	shell_escape(const std::string_view s)	46✔
277	{
278	if (s.empty()) {	46✔
279	return "''";	2✔
280	}
281
282	for (const auto c : s) {	201✔
283	// Conservative list of safe values; better safe than sorry
284	if (!isalnum(c) && c != '_' && c != '.' && c != '/' && c != '-') {	96✔
285	return log_escape(s);	30✔
286	}
287	}
288
289	return std::string{ s };	30✔
290	}
291
292	std::string
293	log_escape(const std::string_view s)	46✔
294	{
295	std::string out;	46✔
296	out.push_back('\'');	46✔
297
298	for (const auto c : s) {	410✔
299	switch (c) {	272✔
300	case '\'':	4✔
301	out.append("\\'");	4✔
302	break;
303	case '\\':	2✔
304	out.append("\\\\");	2✔
305	break;
306	case '\b':	2✔
307	out.append("\\b");	2✔
308	break;
309	case '\f':	2✔
310	out.append("\\f");	2✔
311	break;
312	case '\n':	2✔
313	out.append("\\n");	2✔
314	break;
315	case '\r':	2✔
316	out.append("\\r");	2✔
317	break;
318	case '\t':	2✔
319	out.append("\\t");	2✔
320	break;
321	default:	256✔
322	if (!std::isprint(c)) {	256✔
323	std::ostringstream ss;	7✔
324	ss << "\\x" << std::hex << static_cast<int>(c);	14✔
325
326	out.append(ss.str());	28✔
327
328	} else {	7✔
329	out.push_back(c);	249✔
330	}
331	}
332	}
333
334	out.push_back('\'');	46✔
335
336	return out;	46✔
337	}	×
338
339	std::string
340	shell_escape_command(const string_vec& values)	2✔
341	{
342	std::ostringstream ss;	2✔
343	for (size_t i = 0; i < values.size(); ++i) {	14✔
344	if (i) {	5✔
345	ss << ' ';	4✔
346	}
347
348	ss << shell_escape(values.at(i));	25✔
349	}
350
351	return ss.str();	4✔
352	}	2✔
353
354	std::string
355	format_thousand_sep(size_t count)	5✔
356	{
357	if (!count) {	5✔
358	return "0";	2✔
359	}
360
361	std::string ss;	4✔
362	for (size_t i = 0; count; ++i) {	24✔
363	ss.push_back('0' + (count % 10));	20✔
364	count /= 10;	20✔
365	if (count && i && i % 3 == 2) {	20✔
366	ss.push_back(',');	4✔
367	}
368	}
369
370	std::reverse(ss.begin(), ss.end());	12✔
371
372	return ss;	4✔
373	}	5✔
374
375	std::string
376	format_rough_number(size_t value, size_t out_digits)	37✔
377	{
378	AR_REQUIRE(out_digits > 0);	41✔
379	if (value == 0) {	36✔
380	return "0";	6✔
381	}
382
383	auto rounded = static_cast<double>(value);	33✔
384	auto in_digits = static_cast<size_t>(std::log10(rounded));	33✔
385	if (out_digits > in_digits) {	33✔
386	return std::to_string(value);	5✔
387	}
388
389	// Round to desired number of significant digits
390	const auto tmp = std::pow(10, in_digits - out_digits + 1);	28✔
391	rounded = std::round(rounded / tmp) * tmp;	28✔
392
393	// Rounding up may result in the number of digits increasing
394	in_digits = static_cast<size_t>(std::log10(rounded));	28✔
395
396	const std::string units = "KMGTP";	56✔
397	const size_t unit = std::min<size_t>(units.size(), in_digits / 3);	84✔
398	const double scaled = rounded / std::pow(10.0, unit * 3);	28✔
399	const size_t precision =	28✔
400	out_digits - std::min<size_t>(out_digits, in_digits - unit * 3 + 1);	56✔
401
402	std::ostringstream ss;	28✔
403	ss << std::fixed << std::setprecision(precision) << scaled;	84✔
404
405	if (unit) {	28✔
406	ss << " " << units.at(unit - 1);	52✔
407	}
408
409	return ss.str();	28✔
410	}	64✔
411
412	std::string
413	format_fraction(uint64_t num, uint64_t denom, size_t precision)	13✔
414	{
415	if (denom) {	13✔
416	const double fraction = static_cast<double>(num) / denom;	9✔
417
418	std::ostringstream ss;	9✔
419	ss << std::fixed << std::setprecision(precision) << fraction;	27✔
420
421	return ss.str();	9✔
422	} else {	9✔
423	return "NA";	8✔
424	}
425	}
426
427	std::string
428	format_percentage(uint64_t num, uint64_t denom, size_t precision)	6✔
429	{
430	return format_fraction(num * 100, denom, precision);	6✔
431	}
432
433	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #39

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