MikkelSchubert / adapterremoval / #37

Committed 28 Jul 2024 09:48PM UTC coverage: 86.839% (-0.4%) from 87.26%

Build # #37

Build Type

push

travis-ci

Committed by

MikkelSchubert

Commit Message

allow bool arguments without a sink variable

Run Details

2151 of 2477 relevant lines covered (86.84%)

16470.77 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

99.05

/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& s, const std::string& 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(const std::string& str)
{
  std::string lowercase = str;
  for (auto& current : lowercase) {
    current = to_lower(current);
  }

  return lowercase;
}

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

  return uppercase;
}

/** Returns true if str1 ends with str2 (case sensitive) */
bool
ends_with(const std::string& str1, const std::string& str2)
{
  if (str1.size() < str2.size()) {
    return false;
  }

  auto it1 = str1.rbegin();
  auto it2 = str2.rbegin();
  for (; it2 != str2.rend(); ++it1, ++it2) {
    if (*it1 != *it2) {
      return false;
    }
  }

  return true;
}

string_vec
split_lines(const std::string& text)
{
  string_vec lines;

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

    lines.push_back(text.substr(start, end - start));

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

  return lines;
}

std::string
indent_lines(const std::string& 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& 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& 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 s;
}

std::string
log_escape(const std::string& 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)	85✔
39	{
40	const std::string indentation(n_indent, ' ');	170✔
41	for (auto it = lines.begin(); it != lines.end(); ++it) {	673✔
42	if (!it->empty() && (indent_first \|\| it != lines.begin())) {	324✔
43	it->insert(0, indentation);	161✔
44	}
45	}
46
47	return lines;	255✔
48	}	85✔
49
50	} // namespace
51
52	size_t
53	levenshtein(const std::string& s, const std::string& t)	17✔
54	{
55	std::vector<size_t> v0(t.size() + 1, 0);	34✔
56	std::vector<size_t> v1(t.size() + 1, 0);	34✔
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) {	116✔
63	v1.at(0) = i + 1;	82✔
64
65	for (size_t j = 0; j < t.size(); ++j) {	428✔
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(const std::string& str)	14✔
126	{
127	std::string lowercase = str;	14✔
128	for (auto& current : lowercase) {	200✔
129	current = to_lower(current);	56✔
130	}
131
132	return lowercase;	14✔
133	}
134
135	std::string
136	to_upper(const std::string& str)	2✔
137	{
138	std::string uppercase = str;	2✔
139	for (auto& current : uppercase) {	44✔
140	current = to_upper(current);	16✔
141	}
142
143	return uppercase;	2✔
144	}
145
146	/** Returns true if str1 ends with str2 (case sensitive) */
147	bool
148	ends_with(const std::string& str1, const std::string& str2)	13✔
149	{
150	if (str1.size() < str2.size()) {	39✔
151	return false;
152	}
153
154	auto it1 = str1.rbegin();	11✔
155	auto it2 = str2.rbegin();	11✔
156	for (; it2 != str2.rend(); ++it1, ++it2) {	113✔
157	if (it1 != it2) {	63✔
158	return false;
159	}
160	}
161
162	return true;
163	}
164
165	string_vec
166	split_lines(const std::string& text)	154✔
167	{
168	string_vec lines;	154✔
169
170	size_t start = 0;	154✔
171	size_t end = std::string::npos;	154✔
172	do {	176✔
173	end = text.find('\n', start);	176✔
174
175	lines.push_back(text.substr(start, end - start));	528✔
176
177	start = end + 1;	176✔
178	} while (end != std::string::npos);	176✔
179
180	return lines;	154✔
181	}	×
182
183	std::string
184	indent_lines(const std::string& lines, size_t indentation)	11✔
185	{
186	return join_text(indent(split_lines(lines), indentation, true), "\n");	33✔
187	}
188
189	string_vec
190	wrap_text(const std::string& value, size_t max_width, size_t ljust)	109✔
191	{
192	size_t current_width = 0;	109✔
193	size_t current_ljust = 0;	109✔
194	std::istringstream lines_in(value);	109✔
195	string_vec lines_out;	109✔
196
197	std::string substr;	109✔
198	while (lines_in >> substr) {	1,072✔
199	if (current_width) {	427✔
200	if (current_ljust + current_width + 1 + substr.length() > max_width) {	652✔
201	current_ljust = ljust;	28✔
202	lines_out.emplace_back(current_ljust, ' ');	28✔
203	lines_out.back().append(substr);	56✔
204	current_width = substr.length();	56✔
205	} else {
206	lines_out.back().push_back(' ');	596✔
207	lines_out.back().append(substr);	596✔
208	current_width += substr.length() + 1;	596✔
209	}
210	} else {
211	lines_out.push_back(substr);	101✔
212	current_width += substr.length();	202✔
213	}
214	}
215
216	return lines_out;	218✔
217	}	109✔
218
219	///////////////////////////////////////////////////////////////////////////////
220	// Implementations for 'cli_formatter'
221
222	cli_formatter::cli_formatter()	44✔
223	: m_indent_first(true)	44✔
224	, m_ljust(0)	44✔
225	, m_columns(DEFAULT_MAX_COLUMNS)	44✔
226	, m_indentation(4)	44✔
227	{
228	}	44✔
229
230	cli_formatter&
231	cli_formatter::set_column_width(size_t value)	44✔
232	{
233	m_columns = value;	44✔
234
235	return *this;	44✔
236	}
237
238	cli_formatter&
239	cli_formatter::set_ljust(size_t value)	32✔
240	{
241	m_ljust = value;	32✔
242
243	return *this;	32✔
244	}
245
246	cli_formatter&
247	cli_formatter::set_indent(size_t value)	44✔
248	{
249	m_indentation = value;	44✔
250
251	return *this;	44✔
252	}
253
254	cli_formatter&
255	cli_formatter::set_indent_first_line(bool value)	12✔
256	{
257	m_indent_first = value;	12✔
258
259	return *this;	12✔
260	}
261
262	std::string
263	cli_formatter::format(const std::string& value) const	74✔
264	{
265	std::ostringstream lines_out;	74✔
266
267	for (const auto& line : split_lines(value)) {	592✔
268	const auto block = wrap_text(line, m_columns, m_ljust);	74✔
269
270	lines_out << join_text(indent(block, m_indentation, m_indent_first), "\n");	370✔
271	}	148✔
272
273	return lines_out.str();	148✔
274	}	74✔
275
276	std::string
277	shell_escape(const std::string& s)	46✔
278	{
279	if (s.empty()) {	92✔
280	return "''";	2✔
281	}
282
283	for (const auto c : s) {	474✔
284	// Conservative list of safe values; better safe than sorry
285	if (!isalnum(c) && c != '_' && c != '.' && c != '/' && c != '-') {	96✔
286	return log_escape(s);	30✔
287	}
288	}
289
290	return s;	15✔
291	}
292
293	std::string
294	log_escape(const std::string& s)	43✔
295	{
296	std::string out;	43✔
297	out.push_back('\'');	43✔
298
299	for (const auto c : s) {	1,248✔
300	switch (c) {	269✔
301	case '\'':	4✔
302	out.append("\\'");	4✔
303	break;
304	case '\\':	2✔
305	out.append("\\\\");	2✔
306	break;
307	case '\b':	2✔
308	out.append("\\b");	2✔
309	break;
310	case '\f':	2✔
311	out.append("\\f");	2✔
312	break;
313	case '\n':	2✔
314	out.append("\\n");	2✔
315	break;
316	case '\r':	2✔
317	out.append("\\r");	2✔
318	break;
319	case '\t':	2✔
320	out.append("\\t");	2✔
321	break;
322	default:	253✔
323	if (!std::isprint(c)) {	253✔
324	std::ostringstream ss;	7✔
325	ss << "\\x" << std::hex << static_cast<int>(c);	14✔
326
327	out.append(ss.str());	28✔
328
329	} else {	7✔
330	out.push_back(c);	246✔
331	}
332	}
333	}
334
335	out.push_back('\'');	43✔
336
337	return out;	43✔
338	}	×
339
340	std::string
341	shell_escape_command(const string_vec& values)	2✔
342	{
343	std::ostringstream ss;	2✔
344	for (size_t i = 0; i < values.size(); ++i) {	14✔
345	if (i) {	5✔
346	ss << ' ';	4✔
347	}
348
349	ss << shell_escape(values.at(i));	20✔
350	}
351
352	return ss.str();	4✔
353	}	2✔
354
355	std::string
356	format_thousand_sep(size_t count)	5✔
357	{
358	if (!count) {	5✔
359	return "0";	2✔
360	}
361
362	std::string ss;	4✔
363	for (size_t i = 0; count; ++i) {	24✔
364	ss.push_back('0' + (count % 10));	20✔
365	count /= 10;	20✔
366	if (count && i && i % 3 == 2) {	20✔
367	ss.push_back(',');	4✔
368	}
369	}
370
371	std::reverse(ss.begin(), ss.end());	12✔
372
373	return ss;	4✔
374	}	5✔
375
376	std::string
377	format_rough_number(size_t value, size_t out_digits)	37✔
378	{
379	AR_REQUIRE(out_digits > 0);	41✔
380	if (value == 0) {	36✔
381	return "0";	6✔
382	}
383
384	auto rounded = static_cast<double>(value);	33✔
385	auto in_digits = static_cast<size_t>(std::log10(rounded));	33✔
386	if (out_digits > in_digits) {	33✔
387	return std::to_string(value);	5✔
388	}
389
390	// Round to desired number of significant digits
391	const auto tmp = std::pow(10, in_digits - out_digits + 1);	28✔
392	rounded = std::round(rounded / tmp) * tmp;	28✔
393
394	// Rounding up may result in the number of digits increasing
395	in_digits = static_cast<size_t>(std::log10(rounded));	28✔
396
397	const std::string units = "KMGTP";	56✔
398	const size_t unit = std::min<size_t>(units.size(), in_digits / 3);	84✔
399	const double scaled = rounded / std::pow(10.0, unit * 3);	28✔
400	const size_t precision =	28✔
401	out_digits - std::min<size_t>(out_digits, in_digits - unit * 3 + 1);	56✔
402
403	std::ostringstream ss;	28✔
404	ss << std::fixed << std::setprecision(precision) << scaled;	84✔
405
406	if (unit) {	28✔
407	ss << " " << units.at(unit - 1);	52✔
408	}
409
410	return ss.str();	28✔
411	}	64✔
412
413	std::string
414	format_fraction(uint64_t num, uint64_t denom, size_t precision)	13✔
415	{
416	if (denom) {	13✔
417	const double fraction = static_cast<double>(num) / denom;	9✔
418
419	std::ostringstream ss;	9✔
420	ss << std::fixed << std::setprecision(precision) << fraction;	27✔
421
422	return ss.str();	9✔
423	} else {	9✔
424	return "NA";	8✔
425	}
426	}
427
428	std::string
429	format_percentage(uint64_t num, uint64_t denom, size_t precision)	6✔
430	{
431	return format_fraction(num * 100, denom, precision);	6✔
432	}
433
434	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #37

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous