smithlab_cpp/cigar_utils.hpp at master · smithlabcode/smithlab_cpp · GitHub

History

301 lines (268 loc) · 9.64 KB

Raw

100

101

102

103

104

105

106

107

108

109

110

111

112

113

114

115

116

117

118

119

120

121

122

123

124

125

126

127

128

129

130

131

132

133

134

135

136

137

138

139

140

141

142

143

144

145

146

147

148

149

150

151

152

153

154

155

156

157

158

159

160

161

162

163

164

165

166

167

168

169

170

171

172

173

174

175

176

177

178

179

180

181

182

183

184

185

186

187

188

189

190

191

192

193

194

195

196

197

198

199

200

201

202

203

204

205

206

207

208

209

210

211

212

213

214

215

216

217

218

219

220

221

222

223

224

225

226

227

228

229

230

231

232

233

234

235

236

237

238

239

240

241

242

243

244

245

246

247

248

249

250

251

252

253

254

255

256

257

258

259

260

261

262

263

264

265

266

267

268

269

270

271

272

273

274

275

276

277

278

279

280

281

282

283

284

285

286

287

288

289

290

291

292

293

294

295

296

297

298

299

300

301

* Authors: Andrew D. Smith

* This 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 software 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.

#ifndef CIGAR_UTILS_HPP

#define CIGAR_UTILS_HPP

#include <algorithm>

#include <cctype>

#include <cstdio>

#include <initializer_list>

#include <iterator>

#include <string>

inline bool consumes_query(const char op) {

return ((op == 'M') || (op == 'I') || (op == 'S') || (op == '=') ||

(op == 'X'));

}

inline bool consumes_reference(const char op) {

return ((op == 'M') || (op == 'D') || (op == 'N') || (op == '=') ||

(op == 'X'));

}

template <class InItr>

static size_t extract_op_count(InItr &itr, const InItr last) {

size_t x = 0;

while (itr != last && std::isdigit(*itr))

x = x * 10 + (*itr++ - '0');

return x;

}

template <class InputItr>

size_t cigar_total_ops(InputItr itr, const InputItr last) {

size_t op_count = 0;

while (itr != last) {

op_count += extract_op_count(itr, last);

if (itr != last)

*itr++; // eat the op code

}

return op_count;

}

template <class InputItr>

size_t cigar_qseq_ops(InputItr itr, const InputItr last) {

size_t op_count = 0;

while (itr != last) {

const size_t curr_val = extract_op_count(itr, last);

op_count += curr_val * consumes_query(*itr++);

}

return op_count;

}

template <class T> size_t cigar_qseq_ops(const T &cigar) {

return cigar_qseq_ops(std::begin(cigar), std::end(cigar));

}

template <class InputItr>

size_t cigar_rseq_ops(InputItr itr, const InputItr last) {

size_t op_count = 0;

while (itr != last) {

const size_t curr_val = extract_op_count(itr, last);

op_count += curr_val * consumes_reference(*itr++);

}

return op_count;

}

template <class T> constexpr size_t cigar_rseq_ops(const T &cigar) {

return cigar_rseq_ops(std::begin(cigar), std::end(cigar));

}

template <class InputItr>

void reverse_cigar(InputItr left, const InputItr last) {

std::reverse(left, last);

InputItr right(left);

while (left != last) {

right = std::find_if(++right, last, // ++right eats op in rev orientation

[](const char c) { return !std::isdigit(c); });

std::reverse(left, right);

left = right;

}

template <class T> void reverse_cigar(T &cigar) {

reverse_cigar(std::begin(cigar), std::end(cigar));

}

template <class InputItr>

InputItr truncate_cigar(InputItr left, const InputItr last,

const size_t target_ops) {

/* truncate cigar after specified number of total operations */

InputItr right(left);

size_t prev_ops = 0, curr_ops = 0;

char op = '\0';

while (left != last && prev_ops + curr_ops <= target_ops) {

left = right;

prev_ops += curr_ops;

curr_ops = extract_op_count(right, last);

op = *right++; // cigar always ends with an op

}

if (left != last && target_ops > prev_ops)

left += snprintf(&(*left), 16, "%lu%c", target_ops - prev_ops, op);

return left;

}

template <class InputItr>

InputItr truncate_cigar_q(InputItr left, const InputItr last,

const size_t target_ops) {

/* truncate cigar after specified number of query operations */

InputItr right(left);

size_t prev_ops = 0, curr_ops = 0;

char op = '\0';

while (left != last && prev_ops + curr_ops <= target_ops) {

left = right;

prev_ops += curr_ops;

curr_ops = extract_op_count(right, last);

op = *right++; // cigar always ends with an op

if (!consumes_query(op))

curr_ops = 0;

}

if (left != last && target_ops > prev_ops)

left += snprintf(&(*left), 16, "%lu%c", target_ops - prev_ops, op);

return left;

}

template <class T> void truncate_cigar_q(T &cigar, const size_t target_ops) {

/* truncate cigar after specified number of query operations */

auto c_beg(std::begin(cigar));

auto updated_end = truncate_cigar_q(c_beg, std::end(cigar), target_ops);

cigar.resize(std::distance(c_beg, updated_end));

}

template <class InputItr>

InputItr truncate_cigar_r(InputItr left, const InputItr last,

const size_t target_ops) {

/* truncate cigar after specified number of reference operations */

InputItr right(left);

size_t prev_ops = 0, curr_ops = 0;

char op = '\0';

while (left != last && prev_ops + curr_ops <= target_ops) {

left = right;

prev_ops += curr_ops;

curr_ops = extract_op_count(right, last);

op = *right++; // cigar always ends with an op

if (!consumes_reference(op))

curr_ops = 0;

}

if (left != last && target_ops > prev_ops)

left += snprintf(&(*left), 16, "%lu%c", target_ops - prev_ops, op);

return left;

}

template <class T> void truncate_cigar_r(T &cigar, const size_t target_ops) {

/* truncate cigar after specified number of reference operations */

auto c_beg(std::begin(cigar));

auto updated_end = truncate_cigar_r(c_beg, std::end(cigar), target_ops);

cigar.resize(std::distance(c_beg, updated_end));

}

template <class InputItr>

InputItr merge_equal_neighbor_cigar_ops(InputItr rd_itr, const InputItr last) {

/* renders a cigar valid by merging consecutive identical operations */

InputItr wr_itr(rd_itr);

size_t prev_op_count = extract_op_count(rd_itr, last);

char prev_op = *rd_itr++;

while (rd_itr != last) {

const size_t curr_op_count = extract_op_count(rd_itr, last);

const char op = *rd_itr++;

if (op != prev_op) {

wr_itr += snprintf(&(*wr_itr), 16, "%lu%c", prev_op_count, prev_op);

prev_op_count = 0;

}

prev_op_count += curr_op_count;

prev_op = op;

}

wr_itr += snprintf(&(*wr_itr), 16, "%lu%c", prev_op_count, prev_op);

return wr_itr;

}

template <class T> void merge_equal_neighbor_cigar_ops(T &cigar) {

/* renders a cigar valid by merging consecutive identical operations */

auto c_beg(std::begin(cigar));

auto updated_end = merge_equal_neighbor_cigar_ops(c_beg, std::end(cigar));

cigar.resize(std::distance(c_beg, updated_end));

}

template <class InputItr>

void internal_S_to_M(InputItr rd_itr, const InputItr last) {

/* converts internal soft-clip (S) symbols into match/mismatch (M) symbols */

extract_op_count(rd_itr, last); // move past first op count

rd_itr++; // move past first op

while (rd_itr != last) {

extract_op_count(rd_itr, last); // past curr op count

auto curr_op = rd_itr++; // save curr op iterator

if (rd_itr != last && *curr_op == 'S') {

*curr_op = 'M';

}

template <class T> void internal_S_to_M(T &cigar) {

/* converts internal soft-clip (S) symbols into match/mismatch (M) symbols */

internal_S_to_M(std::begin(cigar), std::end(cigar));

}

template <class T> void terminal_S_to_M(T &cigar) {

/* converts a terminal soft-clip symbol to a match/mismatch (M) symbol */

if (cigar.back() == 'S')

cigar.back() = 'M';

}

template <class InputItr>

void initial_S_to_M(InputItr rd_itr, const InputItr last) {

/* converts an initial soft-clip symbol to a match/mismatch (M) symbol */

extract_op_count(rd_itr, last);

if (*rd_itr == 'S')

*rd_itr = 'M';

}

template <class T> void initial_S_to_M(T &cigar) {

/* converts an initial soft-clip symbol to a match/mismatch (M) symbol */

initial_S_to_M(std::begin(cigar), std::end(cigar));

}

template <class InputItr>

size_t get_soft_clip_size(InputItr rd_itr, const InputItr last) {

/* determine the total size of the soft-clips at both ends */

size_t r = 0;

size_t curr_op_count = extract_op_count(rd_itr, last);

if (*rd_itr++ == 'S')

r += curr_op_count;

char curr_op = '\0';

while (rd_itr != last) {

curr_op_count = extract_op_count(rd_itr, last);

curr_op = *rd_itr++;

}

return (curr_op == 'S') ? r + curr_op_count : r;

}

template <class T> constexpr size_t get_soft_clip_size(T &cigar) {

/* determine the total size of the soft-clips at both ends */

return get_soft_clip_size(std::begin(cigar), std::end(cigar));

}

template <class InputItr>

size_t get_soft_clip_size_start(InputItr rd_itr, const InputItr last) {

/* determine the size of the soft-clip at the start of cigar */

const size_t curr_op_count = extract_op_count(rd_itr, last);

return (*rd_itr == 'S') ? curr_op_count : 0;

}

template <class T> constexpr size_t get_soft_clip_size_start(T &cigar) {

/* determine the size of the soft-clip at the start of cigar */

return get_soft_clip_size_start(std::begin(cigar), std::end(cigar));

}

// turns cigar symbols into compressed format

template <class T1, class T2>

void compress_cigar(T1 c_itr, const T1 c_end, T2 &cigar) {

/* convert a sequence of cigar symbols into a valid cigar string */

const size_t N = cigar.size();

unsigned j = 0, n = 0;

char op = *c_itr;

for (; c_itr != c_end; ++c_itr, ++n) {

if (*c_itr != op) {

j += snprintf(&cigar[j], N - j, "%d%c", n, op);

op = *c_itr;

n = 0;

}

j += snprintf(&cigar[j], N - j, "%d%c", n, op);

cigar.resize(j);

}

// turns a cigar string into a string of cigar symbols

template <class T1, class T2>

void uncompress_cigar(T1 c_itr, const T1 c_end, T2 &cigar) {

/* convert a valid cigar string into a sequence of cigar symbols */

cigar.clear(); // ADS: should this be assumed?

while (c_itr != c_end) {

const size_t op_count = extract_op_count(c_itr, c_end);

fill_n(std::back_inserter(cigar), op_count, *c_itr++);

}

void apply_cigar(const std::string &cigar, std::string &to_inflate,

const char inflation_symbol = 'N');

#endif

smithlab_cpp/cigar_utils.hpp at master · smithlabcode/smithlab_cpp · GitHub

Uh oh!

Expand file tree

Breadcrumbs

cigar_utils.hpp

Latest commit

History

Breadcrumbs

cigar_utils.hpp

File metadata and controls