| 1 |
/* |
| 2 |
* fusions.cpp |
| 3 |
* TopHat |
| 4 |
*/ |
| 5 |
|
| 6 |
#ifdef HAVE_CONFIG_H |
| 7 |
#include <config.h> |
| 8 |
#else |
| 9 |
#define PACKAGE_VERSION "INTERNAL" |
| 10 |
#define SVN_REVISION "XXX" |
| 11 |
#endif |
| 12 |
|
| 13 |
|
| 14 |
#include <cassert> |
| 15 |
#include <cstdio> |
| 16 |
#include <cstring> |
| 17 |
#include <vector> |
| 18 |
#include <string> |
| 19 |
#include <map> |
| 20 |
#include <algorithm> |
| 21 |
#include <set> |
| 22 |
#include <stdexcept> |
| 23 |
#include <iostream> |
| 24 |
#include <fstream> |
| 25 |
#include <seqan/sequence.h> |
| 26 |
#include <seqan/find.h> |
| 27 |
#include <seqan/file.h> |
| 28 |
#include <seqan/modifier.h> |
| 29 |
#include <seqan/align.h> |
| 30 |
#include <getopt.h> |
| 31 |
|
| 32 |
#include "common.h" |
| 33 |
#include "bwt_map.h" |
| 34 |
#include "junctions.h" |
| 35 |
#include "fusions.h" |
| 36 |
#include "fragments.h" |
| 37 |
#include "wiggles.h" |
| 38 |
#include "tokenize.h" |
| 39 |
#include "reads.h" |
| 40 |
|
| 41 |
#include "inserts.h" |
| 42 |
|
| 43 |
// daehwan - replace this with that of SeqAn |
| 44 |
int difference(const string& first, const string& second) |
| 45 |
{ |
| 46 |
int len = seqan::length(first); |
| 47 |
if (len != (int)seqan::length(second)) |
| 48 |
return 0; |
| 49 |
|
| 50 |
int min_value = 10000; |
| 51 |
short value1[1024] = {0,}; |
| 52 |
short value2[1024] = {0,}; |
| 53 |
|
| 54 |
short* curr = value1; |
| 55 |
short* prev = value2; |
| 56 |
|
| 57 |
for (int j = 0; j < len; ++j) |
| 58 |
{ |
| 59 |
for (int i = 0; i < len; ++i) |
| 60 |
{ |
| 61 |
int value = 10000; |
| 62 |
int match = first[i] == second[j] ? 0 : 1; |
| 63 |
|
| 64 |
// right |
| 65 |
if (i == 0) |
| 66 |
value = j * 2 + match; |
| 67 |
else if (j > 0) |
| 68 |
value = prev[i] + 2; |
| 69 |
|
| 70 |
int temp_value = 10000; |
| 71 |
|
| 72 |
// down |
| 73 |
if (j == 0) |
| 74 |
temp_value = i * 2 + match; |
| 75 |
else if (i > 0) |
| 76 |
temp_value = curr[i-1] + 2; |
| 77 |
|
| 78 |
if (temp_value < value) |
| 79 |
value = temp_value; |
| 80 |
|
| 81 |
// match |
| 82 |
if (i > 0 && j > 0) |
| 83 |
temp_value = prev[i-1] + match; |
| 84 |
|
| 85 |
if (temp_value < value) |
| 86 |
value = temp_value; |
| 87 |
|
| 88 |
curr[i] = value; |
| 89 |
|
| 90 |
if ((i == len - 1 || j == len - 1) && value < min_value) |
| 91 |
min_value = value; |
| 92 |
} |
| 93 |
|
| 94 |
short* temp = prev; |
| 95 |
prev = curr; |
| 96 |
curr = temp; |
| 97 |
} |
| 98 |
|
| 99 |
return min_value; |
| 100 |
} |
| 101 |
|
| 102 |
|
| 103 |
/** |
| 104 |
* Add fusions from an alignment to an FusionSet. |
| 105 |
* This will look for fusion in the alignment specified by bh. |
| 106 |
* @param bh The bowtie hit to be used to specify alignment infromation. |
| 107 |
* @param fusions The FusionSet that will be updated with the insertion information from teh alignment. |
| 108 |
*/ |
| 109 |
void fusions_from_alignment(const BowtieHit& bh, |
| 110 |
FusionSet& fusions, |
| 111 |
RefSequenceTable& rt, |
| 112 |
bool update_stat) |
| 113 |
{ |
| 114 |
RefSequenceTable::Sequence* ref_str1 = rt.get_seq(bh.ref_id()); |
| 115 |
RefSequenceTable::Sequence* ref_str2 = rt.get_seq(bh.ref_id2()); |
| 116 |
|
| 117 |
if (!ref_str1 || !ref_str2) |
| 118 |
return; |
| 119 |
|
| 120 |
vector<Fusion> new_fusions; |
| 121 |
fusions_from_spliced_hit(bh, new_fusions); |
| 122 |
|
| 123 |
for(size_t i = 0; i < new_fusions.size(); ++i) |
| 124 |
{ |
| 125 |
Fusion fusion = new_fusions[i]; |
| 126 |
const vector<CigarOp>& cigars = bh.cigar(); |
| 127 |
|
| 128 |
/* |
| 129 |
* Assume read is in the same direction as fusion. |
| 130 |
*/ |
| 131 |
|
| 132 |
// Find the position of Fusion. |
| 133 |
size_t fusion_pos = 0; |
| 134 |
for (; fusion_pos < cigars.size(); ++fusion_pos) |
| 135 |
{ |
| 136 |
CigarOpCode opcode = cigars[fusion_pos].opcode; |
| 137 |
if (opcode == FUSION_FF || opcode == FUSION_FR || opcode == FUSION_RF || opcode == FUSION_RR) |
| 138 |
break; |
| 139 |
} |
| 140 |
|
| 141 |
if (fusion_pos <= 0 || fusion_pos + 1 >= cigars.size()) |
| 142 |
continue; |
| 143 |
|
| 144 |
// For left bases, |
| 145 |
size_t left_pos = 0; |
| 146 |
for (int j = (int)fusion_pos - 1; j >= 0; --j) |
| 147 |
{ |
| 148 |
const CigarOp& cigar = cigars[j]; |
| 149 |
switch (cigar.opcode) |
| 150 |
{ |
| 151 |
case MATCH: |
| 152 |
case mATCH: |
| 153 |
case REF_SKIP: |
| 154 |
case rEF_SKIP: |
| 155 |
case DEL: |
| 156 |
case dEL: |
| 157 |
left_pos += cigar.length; |
| 158 |
break; |
| 159 |
default: |
| 160 |
break; |
| 161 |
} |
| 162 |
} |
| 163 |
|
| 164 |
// For right bases, |
| 165 |
size_t right_pos = 0; |
| 166 |
for (size_t j = fusion_pos + 1; j < cigars.size(); ++j) |
| 167 |
{ |
| 168 |
const CigarOp& cigar = cigars[j]; |
| 169 |
switch (cigar.opcode) |
| 170 |
{ |
| 171 |
case MATCH: |
| 172 |
case mATCH: |
| 173 |
case REF_SKIP: |
| 174 |
case rEF_SKIP: |
| 175 |
case DEL: |
| 176 |
case dEL: |
| 177 |
right_pos += cigar.length; |
| 178 |
break; |
| 179 |
default: |
| 180 |
break; |
| 181 |
} |
| 182 |
} |
| 183 |
|
| 184 |
if (left_pos < fusion_anchor_length || right_pos < fusion_anchor_length) |
| 185 |
continue; |
| 186 |
|
| 187 |
FusionSet::iterator itr = fusions.find(fusion); |
| 188 |
if (itr != fusions.end()) |
| 189 |
{ |
| 190 |
itr->second.count += 1; |
| 191 |
} |
| 192 |
else |
| 193 |
{ |
| 194 |
assert(fusion.refid1 != 0xFFFFFFFF); |
| 195 |
FusionStat fusionStat; |
| 196 |
fusionStat.count = 1; |
| 197 |
fusions[fusion] = fusionStat; |
| 198 |
|
| 199 |
itr = fusions.find(fusion); |
| 200 |
|
| 201 |
if (!update_stat) |
| 202 |
{ |
| 203 |
/* |
| 204 |
* make a reversed fusion. |
| 205 |
* this is necessary to detect reads that contradict the fusion. |
| 206 |
*/ |
| 207 |
|
| 208 |
FusionStat fusionStat_rev; |
| 209 |
fusionStat_rev.count = 1; |
| 210 |
fusionStat_rev.reversed = true; |
| 211 |
|
| 212 |
Fusion fusion_rev(fusion.refid2, fusion.refid1, fusion.right, fusion.left, fusion.dir); |
| 213 |
fusions[fusion_rev] = fusionStat_rev; |
| 214 |
} |
| 215 |
} |
| 216 |
|
| 217 |
if (update_stat) |
| 218 |
{ |
| 219 |
if (itr->second.chr1_seq.length() <= 0) |
| 220 |
{ |
| 221 |
size_t len = 100; |
| 222 |
size_t half_len = len / 2; |
| 223 |
size_t increase = 20; |
| 224 |
|
| 225 |
if (fusion.left >= half_len && fusion.left + half_len <= seqan::length(*ref_str1) && |
| 226 |
fusion.right >= half_len && fusion.right + half_len <= seqan::length(*ref_str2)) |
| 227 |
{ |
| 228 |
seqan::Dna5String left, right; |
| 229 |
|
| 230 |
if (fusion.dir == FUSION_RF || fusion.dir == FUSION_RR) |
| 231 |
{ |
| 232 |
left = seqan::infix(*ref_str1, fusion.left - half_len, fusion.left + half_len); |
| 233 |
seqan::reverseComplement(left); |
| 234 |
} |
| 235 |
else |
| 236 |
left = seqan::infix(*ref_str1, fusion.left - half_len + 1, fusion.left + half_len + 1); |
| 237 |
|
| 238 |
if (fusion.dir == FUSION_FR || fusion.dir == FUSION_RR) |
| 239 |
{ |
| 240 |
right = seqan::infix(*ref_str2, fusion.right - half_len + 1, fusion.right + half_len + 1); |
| 241 |
seqan::reverseComplement(right); |
| 242 |
} |
| 243 |
else |
| 244 |
right = seqan::infix(*ref_str2, fusion.right - half_len, fusion.right + half_len); |
| 245 |
|
| 246 |
itr->second.chr1_seq = DnaString_to_string(left); |
| 247 |
itr->second.chr2_seq = DnaString_to_string(right); |
| 248 |
|
| 249 |
for (size_t j = 0; j < 5; ++j) |
| 250 |
{ |
| 251 |
size_t pos = (5 - j - 1) * increase / 2; |
| 252 |
const string& left_sub = itr->second.chr1_seq.substr(pos, (j+1) * increase); |
| 253 |
const string& right_sub = itr->second.chr2_seq.substr(pos, (j+1) * increase); |
| 254 |
|
| 255 |
itr->second.diffs.push_back(difference(left_sub, right_sub)); |
| 256 |
} |
| 257 |
} |
| 258 |
} |
| 259 |
|
| 260 |
assert (bh.ref_id() == itr->first.refid1); |
| 261 |
|
| 262 |
itr->second.left_ext = max((size_t)itr->second.left_ext, left_pos); |
| 263 |
itr->second.right_ext = max((size_t)itr->second.right_ext, right_pos); |
| 264 |
|
| 265 |
for (size_t k = 0; k < left_pos && k < itr->second.left_bases.size(); ++k) |
| 266 |
{ |
| 267 |
++(itr->second.left_bases[k]); |
| 268 |
} |
| 269 |
|
| 270 |
for (size_t k = 0; k < right_pos && k < itr->second.right_bases.size(); ++k) |
| 271 |
{ |
| 272 |
++(itr->second.right_bases[k]); |
| 273 |
} |
| 274 |
} |
| 275 |
} |
| 276 |
} |
| 277 |
|
| 278 |
void unsupport_fusions(const BowtieHit& bh, FusionSet& fusions, const FusionSet& fusions_ref) |
| 279 |
{ |
| 280 |
if (bh.fusion_opcode() != FUSION_NOTHING || bh.is_spliced() || bh.read_len() < 40) |
| 281 |
return; |
| 282 |
|
| 283 |
FusionSet::const_iterator lb, ub; |
| 284 |
|
| 285 |
uint32_t left = bh.left() + 20; |
| 286 |
uint32_t right = bh.right() - 20; |
| 287 |
|
| 288 |
lb = fusions_ref.upper_bound(Fusion(0u, 0u, left, 0)); |
| 289 |
ub = fusions_ref.lower_bound(Fusion(0xffffffffu, 0xffffffffu, right, 0xffffffffu)); |
| 290 |
while (lb != ub && lb != fusions_ref.end()) |
| 291 |
{ |
| 292 |
if (lb->first.refid1 == bh.ref_id()) |
| 293 |
{ |
| 294 |
// daehwan |
| 295 |
#if 0 |
| 296 |
// MCF-7 RPS6KB1 17:57970443-58027925:1 TMEM49 17:57784863-57917950:1 |
| 297 |
if ((lb->first.left == 57992061 && lb->first.right == 57917126) || |
| 298 |
(lb->first.left == 57917126 && lb->first.right == 57992061)) |
| 299 |
{ |
| 300 |
const char* dir_str = "ff"; |
| 301 |
if (lb->first.dir == FUSION_FR) |
| 302 |
dir_str = "fr"; |
| 303 |
else if (lb->first.dir == FUSION_RF) |
| 304 |
dir_str = "rf"; |
| 305 |
|
| 306 |
cout << "fusion: " << lb->first.left << "-" << lb->first.right << endl; |
| 307 |
cout << dir_str << endl; |
| 308 |
cout << bh.insert_id() << ": " << bh.left() << "-" << bh.right() << "\t"; |
| 309 |
cout << print_cigar(bh.cigar()) << " " << (int)bh.edit_dist() << endl; |
| 310 |
cout << bh.seq() << endl; |
| 311 |
cout << bh.qual() << endl; |
| 312 |
cout << endl; |
| 313 |
} |
| 314 |
#endif |
| 315 |
|
| 316 |
FusionSet::iterator itr; |
| 317 |
if (lb->second.reversed) |
| 318 |
itr = fusions.find(Fusion(lb->first.refid2, lb->first.refid1, lb->first.right, lb->first.left, lb->first.dir)); |
| 319 |
else |
| 320 |
itr = fusions.find(lb->first); |
| 321 |
|
| 322 |
if (itr == fusions.end()) |
| 323 |
{ |
| 324 |
FusionStat fusionStat; |
| 325 |
fusionStat.unsupport_count = 1; |
| 326 |
fusions[lb->first] = fusionStat; |
| 327 |
} |
| 328 |
else |
| 329 |
++(itr->second.unsupport_count); |
| 330 |
} |
| 331 |
|
| 332 |
++lb; |
| 333 |
} |
| 334 |
} |
| 335 |
|
| 336 |
/** |
| 337 |
*/ |
| 338 |
void print_fusions(FILE* fusions_out, FusionSet& fusions, RefSequenceTable& ref_sequences) |
| 339 |
{ |
| 340 |
// fprintf(fusions_out, "track name=fusions description=\"TopHat fusions\"\n"); |
| 341 |
|
| 342 |
vector<Fusion> vFusion; |
| 343 |
for (FusionSet::iterator itr = fusions.begin(); itr != fusions.end(); ++itr) |
| 344 |
{ |
| 345 |
vFusion.push_back(itr->first); |
| 346 |
} |
| 347 |
sort(vFusion.begin(), vFusion.end()); |
| 348 |
|
| 349 |
for (size_t i = 0; i < vFusion.size(); ++i) |
| 350 |
{ |
| 351 |
FusionSet::iterator itr = fusions.find(vFusion[i]); |
| 352 |
int counts = itr->second.count; |
| 353 |
if (counts <= 0 || itr->second.reversed) |
| 354 |
continue; |
| 355 |
|
| 356 |
const char* dir = ""; |
| 357 |
if (itr->first.dir == FUSION_FF) |
| 358 |
dir = "ff"; |
| 359 |
else if(itr->first.dir == FUSION_FR) |
| 360 |
dir = "fr"; |
| 361 |
else if(itr->first.dir == FUSION_RF) |
| 362 |
dir = "rf"; |
| 363 |
else |
| 364 |
dir = "rr"; |
| 365 |
|
| 366 |
assert (itr->second.left_bases.size() == itr->second.right_bases.size()); |
| 367 |
|
| 368 |
float symm = 0.0f; |
| 369 |
for (uint32_t i = 0; i < itr->second.left_bases.size(); ++i) |
| 370 |
{ |
| 371 |
float term = ((int)itr->second.left_bases[i] - (int)itr->second.right_bases[i]) / (float)counts; |
| 372 |
symm += (term * term); |
| 373 |
} |
| 374 |
|
| 375 |
fprintf(fusions_out, "%s-%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%.6f", |
| 376 |
ref_sequences.get_name(itr->first.refid1), |
| 377 |
ref_sequences.get_name(itr->first.refid2), |
| 378 |
itr->first.left, |
| 379 |
itr->first.right, |
| 380 |
dir, |
| 381 |
counts, |
| 382 |
itr->second.pair_count, |
| 383 |
itr->second.pair_count_fusion, |
| 384 |
itr->second.unsupport_count, |
| 385 |
itr->second.left_ext, |
| 386 |
itr->second.right_ext, |
| 387 |
symm); |
| 388 |
|
| 389 |
fprintf(fusions_out, "\t@\t"); |
| 390 |
|
| 391 |
for (uint32_t i = 0; i < itr->second.diffs.size(); ++i) |
| 392 |
{ |
| 393 |
fprintf(fusions_out, "%d ", itr->second.diffs[i]); |
| 394 |
} |
| 395 |
|
| 396 |
fprintf(fusions_out, "\t@\t"); |
| 397 |
|
| 398 |
uint32_t half_length = itr->second.chr1_seq.length() / 2; |
| 399 |
fprintf(fusions_out, "%s %s\t@\t", itr->second.chr1_seq.substr(0, half_length).c_str(), itr->second.chr1_seq.substr(half_length).c_str()); |
| 400 |
fprintf(fusions_out, "%s %s\t@\t", itr->second.chr2_seq.substr(0, half_length).c_str(), itr->second.chr2_seq.substr(half_length).c_str()); |
| 401 |
|
| 402 |
for (uint32_t i = 0; i < itr->second.left_bases.size(); ++i) |
| 403 |
{ |
| 404 |
fprintf(fusions_out, "%d ", itr->second.left_bases[i]); |
| 405 |
} |
| 406 |
|
| 407 |
fprintf(fusions_out, "\t@\t"); |
| 408 |
|
| 409 |
for (uint32_t i = 0; i < itr->second.right_bases.size(); ++i) |
| 410 |
{ |
| 411 |
fprintf(fusions_out, "%d ", itr->second.right_bases[i]); |
| 412 |
} |
| 413 |
|
| 414 |
fprintf(fusions_out, "\t@\t"); |
| 415 |
|
| 416 |
sort(itr->second.vPairSupport.begin(), itr->second.vPairSupport.end()); |
| 417 |
for (uint32_t i = 0; i < min((size_t)200, itr->second.vPairSupport.size()); ++i) |
| 418 |
{ |
| 419 |
fprintf(fusions_out, "%d:%d ", itr->second.vPairSupport[i].ldist, itr->second.vPairSupport[i].rdist); |
| 420 |
} |
| 421 |
|
| 422 |
fprintf(fusions_out, "\n"); |
| 423 |
} |
| 424 |
} |
| 425 |
|
| 426 |
/** |
| 427 |
* Extract a list of fusions from a bowtie hit. |
| 428 |
* Given a bowtie hit, extract a vector of insertions. |
| 429 |
* @param bh The bowtie hit to use for alignment information. |
| 430 |
* @param insertions Used to store the resultant vector of insertions. |
| 431 |
*/ |
| 432 |
void fusions_from_spliced_hit(const BowtieHit& bh, vector<Fusion>& fusions, bool auto_sort) |
| 433 |
{ |
| 434 |
const vector<CigarOp>& cigar = bh.cigar(); |
| 435 |
unsigned int positionInGenome = bh.left(); |
| 436 |
|
| 437 |
for(size_t c = 0; c < cigar.size(); ++c) |
| 438 |
{ |
| 439 |
Fusion fusion; |
| 440 |
switch(cigar[c].opcode) |
| 441 |
{ |
| 442 |
case REF_SKIP: |
| 443 |
case MATCH: |
| 444 |
case DEL: |
| 445 |
positionInGenome += cigar[c].length; |
| 446 |
break; |
| 447 |
case rEF_SKIP: |
| 448 |
case mATCH: |
| 449 |
case dEL: |
| 450 |
positionInGenome -= cigar[c].length; |
| 451 |
break; |
| 452 |
case FUSION_FF: |
| 453 |
case FUSION_FR: |
| 454 |
case FUSION_RF: |
| 455 |
case FUSION_RR: |
| 456 |
fusion.dir = cigar[c].opcode; |
| 457 |
if (fusion.dir == FUSION_RF || fusion.dir == FUSION_RR) |
| 458 |
positionInGenome = positionInGenome + 1; |
| 459 |
else |
| 460 |
positionInGenome = positionInGenome - 1; |
| 461 |
|
| 462 |
if (bh.ref_id() < bh.ref_id2() || |
| 463 |
(bh.ref_id() == bh.ref_id2() && positionInGenome < cigar[c].length) || |
| 464 |
!auto_sort) |
| 465 |
{ |
| 466 |
fusion.refid1 = bh.ref_id(); |
| 467 |
fusion.refid2 = bh.ref_id2(); |
| 468 |
fusion.left = positionInGenome; |
| 469 |
fusion.right = cigar[c].length; |
| 470 |
} |
| 471 |
else |
| 472 |
{ |
| 473 |
assert (auto_sort); |
| 474 |
fusion.refid1 = bh.ref_id2(); |
| 475 |
fusion.refid2 = bh.ref_id(); |
| 476 |
fusion.left = cigar[c].length; |
| 477 |
fusion.right = positionInGenome; |
| 478 |
} |
| 479 |
|
| 480 |
fusions.push_back(fusion); |
| 481 |
break; |
| 482 |
default: |
| 483 |
break; |
| 484 |
} |
| 485 |
} |
| 486 |
} |
| 487 |
|
| 488 |
void pair_support(const vector<pair<BowtieHit, BowtieHit> >& best_hits, FusionSet& fusions, FusionSet& fusions_ref) |
| 489 |
{ |
| 490 |
if (best_hits.size() > fusion_multipairs) |
| 491 |
return; |
| 492 |
|
| 493 |
for (size_t i = 0; i < best_hits.size(); ++i) |
| 494 |
{ |
| 495 |
const BowtieHit& lh = best_hits[i].first; |
| 496 |
const BowtieHit& rh = best_hits[i].second; |
| 497 |
|
| 498 |
bool left_fusionSpanned = lh.fusion_opcode() != FUSION_NOTHING; |
| 499 |
bool right_fusionSpanned = rh.fusion_opcode() != FUSION_NOTHING; |
| 500 |
if (left_fusionSpanned && right_fusionSpanned) |
| 501 |
continue; |
| 502 |
|
| 503 |
bool fusionSpanned = left_fusionSpanned || right_fusionSpanned; |
| 504 |
bool fusion_leftSide = false; |
| 505 |
|
| 506 |
uint32_t ref_id1 = lh.ref_id2(); |
| 507 |
uint32_t ref_id2 = rh.ref_id(); |
| 508 |
|
| 509 |
int dir = FUSION_FF; |
| 510 |
if (fusionSpanned) |
| 511 |
{ |
| 512 |
if (left_fusionSpanned) |
| 513 |
dir = lh.fusion_opcode(); |
| 514 |
else |
| 515 |
dir = rh.fusion_opcode(); |
| 516 |
} |
| 517 |
else |
| 518 |
{ |
| 519 |
if (!lh.antisense_align() && !rh.antisense_align()) |
| 520 |
dir = FUSION_FR; |
| 521 |
else if (lh.antisense_align() && rh.antisense_align()) |
| 522 |
dir = FUSION_RF; |
| 523 |
else |
| 524 |
{ |
| 525 |
if (lh.ref_id() == rh.ref_id()) |
| 526 |
{ |
| 527 |
if ((lh.antisense_align() && lh.left() > rh.left()) || |
| 528 |
(!lh.antisense_align() && lh.left() < rh.left())) |
| 529 |
dir = FUSION_FF; |
| 530 |
else |
| 531 |
dir = FUSION_RR; |
| 532 |
} |
| 533 |
else |
| 534 |
{ |
| 535 |
if ((lh.antisense_align() && lh.ref_id() > rh.ref_id()) || |
| 536 |
(!lh.antisense_align() && lh.ref_id() < rh.ref_id())) |
| 537 |
dir = FUSION_FF; |
| 538 |
else |
| 539 |
dir = FUSION_RR; |
| 540 |
} |
| 541 |
} |
| 542 |
} |
| 543 |
|
| 544 |
FusionSet::iterator lb, ub; |
| 545 |
bool unsupport = false; |
| 546 |
|
| 547 |
// int inner_dist = max_report_intron_length * 2; |
| 548 |
|
| 549 |
int inner_dist = 10000; |
| 550 |
int outer_dist = 10000 * 2; |
| 551 |
int max_dist = 10000 * 2; |
| 552 |
int left1 = 0, left2 = 0, right1 = 0, right2 = 0; |
| 553 |
|
| 554 |
if (fusionSpanned) |
| 555 |
{ |
| 556 |
vector<Fusion> new_fusions; |
| 557 |
if (left_fusionSpanned) |
| 558 |
fusions_from_spliced_hit(lh, new_fusions); |
| 559 |
else |
| 560 |
fusions_from_spliced_hit(rh, new_fusions); |
| 561 |
|
| 562 |
Fusion& fusion = new_fusions[0]; |
| 563 |
dir = fusion.dir; |
| 564 |
ref_id1 = fusion.refid1; |
| 565 |
ref_id2 = fusion.refid2; |
| 566 |
|
| 567 |
if (left_fusionSpanned && lh.ref_id() != ref_id2 && lh.ref_id2() != ref_id2) |
| 568 |
unsupport = true; |
| 569 |
|
| 570 |
if (right_fusionSpanned && rh.ref_id() != ref_id1 && rh.ref_id2() != ref_id1) |
| 571 |
unsupport = true; |
| 572 |
|
| 573 |
int temp1, temp2; |
| 574 |
const BowtieHit* fusionHit; |
| 575 |
const BowtieHit* otherHit; |
| 576 |
|
| 577 |
if (left_fusionSpanned) |
| 578 |
{ |
| 579 |
fusionHit = &lh; |
| 580 |
otherHit = &rh; |
| 581 |
} |
| 582 |
else |
| 583 |
{ |
| 584 |
fusionHit = &rh; |
| 585 |
otherHit = &lh; |
| 586 |
} |
| 587 |
|
| 588 |
// check the normal hit (otherHit) is on the left hand side of the fusion. |
| 589 |
if (ref_id1 == ref_id2) |
| 590 |
{ |
| 591 |
if (dir == FUSION_FF || dir == FUSION_FR) |
| 592 |
fusion_leftSide = otherHit->left() < fusionHit->left(); |
| 593 |
else if (dir == FUSION_RF) |
| 594 |
fusion_leftSide = otherHit->left() < fusionHit->right(); |
| 595 |
else |
| 596 |
fusion_leftSide = otherHit->right() > fusionHit->left(); |
| 597 |
} |
| 598 |
else |
| 599 |
fusion_leftSide = fusionHit->ref_id() == otherHit->ref_id(); |
| 600 |
|
| 601 |
// ***** |
| 602 |
// daehwan - make sure what '+' and '-' really mean for FF, FR, RF, RR cases |
| 603 |
// ***** |
| 604 |
if ((dir != FUSION_RF && dir != FUSION_RR) && fusionHit->antisense_align() && (!fusion_leftSide || otherHit->antisense_align())) |
| 605 |
unsupport = true; |
| 606 |
|
| 607 |
if ((dir != FUSION_FR && dir != FUSION_RR) && !fusionHit->antisense_align() && (fusion_leftSide || !otherHit->antisense_align())) |
| 608 |
unsupport = true; |
| 609 |
|
| 610 |
if ((dir == FUSION_FR || dir == FUSION_RR) && !fusionHit->antisense_align() && (fusion_leftSide || otherHit->antisense_align())) |
| 611 |
unsupport = true; |
| 612 |
|
| 613 |
if ((dir == FUSION_RF || dir == FUSION_RR) && fusionHit->antisense_align() && (!fusion_leftSide || !otherHit->antisense_align())) |
| 614 |
unsupport = true; |
| 615 |
|
| 616 |
temp1 = otherHit->left(); |
| 617 |
temp2 = otherHit->right(); |
| 618 |
|
| 619 |
if ((fusion_leftSide && dir == FUSION_RF) || (!fusion_leftSide && dir != FUSION_FR)) |
| 620 |
{ |
| 621 |
temp2 = temp1 + inner_dist; |
| 622 |
if (temp1 > outer_dist) |
| 623 |
temp1 = temp1 - outer_dist; |
| 624 |
else |
| 625 |
temp1 = 0; |
| 626 |
} |
| 627 |
else |
| 628 |
{ |
| 629 |
if (temp2 >= inner_dist) |
| 630 |
temp1 = temp2 - inner_dist; |
| 631 |
else |
| 632 |
temp1 = 0; |
| 633 |
|
| 634 |
temp2 = temp2 + outer_dist; |
| 635 |
} |
| 636 |
|
| 637 |
if (fusion_leftSide) |
| 638 |
{ |
| 639 |
left1 = temp1; |
| 640 |
left2 = temp2; |
| 641 |
} |
| 642 |
else |
| 643 |
{ |
| 644 |
right1 = temp1; |
| 645 |
right2 = temp2; |
| 646 |
} |
| 647 |
|
| 648 |
lb = fusions_ref.find(fusion); |
| 649 |
ub = fusions_ref.end(); |
| 650 |
|
| 651 |
// daehwan - debug |
| 652 |
#if 0 |
| 653 |
if (fusion.left == 6994359 && fusion.right == 17581683) |
| 654 |
{ |
| 655 |
cout << "daehwan - test - pair_with_fusion: " << lh.insert_id() << endl; |
| 656 |
cout << "edit dist: " << (int)lh.edit_dist() << ", " << (int)rh.edit_dist() << endl; |
| 657 |
const char* dir_str = "ff"; |
| 658 |
if (dir == FUSION_FR) |
| 659 |
dir_str = "fr"; |
| 660 |
else if (dir == FUSION_RF) |
| 661 |
dir_str = "rf"; |
| 662 |
else if (dir == FUSION_RR) |
| 663 |
dir_str = "rr"; |
| 664 |
|
| 665 |
cout << dir_str << " : " << (lh.antisense_align() ? "-" : "+") << " " << (rh.antisense_align() ? "-" : "+") << endl; |
| 666 |
cout << lh.ref_id() << ": " << lh.left() << "-" << lh.right() << endl; |
| 667 |
cout << lh.ref_id2() << ": " << print_cigar(lh.cigar()) << endl; |
| 668 |
cout << rh.ref_id() << ": " << rh.left() << "-" << rh.right() << endl; |
| 669 |
cout << rh.ref_id2() << ": " << print_cigar(rh.cigar()) << endl; |
| 670 |
cout << "found: " << (lb == ub ? "no" : "yes") << endl; |
| 671 |
cout << "unsupport: " << (unsupport ? "yes" : "no") << endl; |
| 672 |
cout << "fusion_left: " << (fusion_leftSide ? "yes" : "no") << endl; |
| 673 |
cout << endl; |
| 674 |
} |
| 675 |
#endif |
| 676 |
} |
| 677 |
else |
| 678 |
{ |
| 679 |
if (dir == FUSION_FF) |
| 680 |
{ |
| 681 |
if (lh.antisense_align()) |
| 682 |
{ |
| 683 |
if (rh.right() >= inner_dist) |
| 684 |
right1 = rh.right() - inner_dist; |
| 685 |
right2 = right1 + outer_dist; |
| 686 |
|
| 687 |
left2 = lh.left() + inner_dist; |
| 688 |
if (left2 > outer_dist) |
| 689 |
left1 = left2 - outer_dist; |
| 690 |
} |
| 691 |
else |
| 692 |
{ |
| 693 |
if (lh.right() >= inner_dist) |
| 694 |
left1 = lh.right() - inner_dist; |
| 695 |
left2 = left1 + outer_dist; |
| 696 |
|
| 697 |
right2 = rh.left() + inner_dist; |
| 698 |
if (right2 > outer_dist) |
| 699 |
right1 = right2 - outer_dist; |
| 700 |
} |
| 701 |
} |
| 702 |
else if (dir == FUSION_FR) |
| 703 |
{ |
| 704 |
if (lh.right() >= inner_dist) |
| 705 |
left1 = lh.right() - inner_dist; |
| 706 |
left2 = left1 + outer_dist; |
| 707 |
|
| 708 |
if (rh.right() >= inner_dist) |
| 709 |
right1 = rh.right() - inner_dist; |
| 710 |
right2 = right1 + outer_dist; |
| 711 |
} |
| 712 |
else if (dir == FUSION_RF) |
| 713 |
{ |
| 714 |
left2 = lh.left() + inner_dist; |
| 715 |
right2 = rh.left() + inner_dist; |
| 716 |
|
| 717 |
if (left2 > outer_dist) |
| 718 |
left1 = left2 - outer_dist; |
| 719 |
|
| 720 |
if (right2 > outer_dist) |
| 721 |
right1 = right2 - outer_dist; |
| 722 |
} |
| 723 |
else // if (dir == FUSION_RR) |
| 724 |
{ |
| 725 |
if (lh.antisense_align()) |
| 726 |
{ |
| 727 |
left2 = lh.left() + inner_dist; |
| 728 |
if (left2 > outer_dist) |
| 729 |
left1 = left2 - outer_dist; |
| 730 |
|
| 731 |
if (rh.right() >= inner_dist) |
| 732 |
right1 = rh.right() - inner_dist; |
| 733 |
right2 = right1 + outer_dist; |
| 734 |
} |
| 735 |
else |
| 736 |
{ |
| 737 |
if (lh.right() >= inner_dist) |
| 738 |
left1 = lh.right() - inner_dist; |
| 739 |
left2 = left1 + outer_dist; |
| 740 |
|
| 741 |
right2 = rh.left() + inner_dist; |
| 742 |
if (right2 > outer_dist) |
| 743 |
right1 = right2 - outer_dist; |
| 744 |
} |
| 745 |
} |
| 746 |
|
| 747 |
// daehwan - debug |
| 748 |
#if 0 |
| 749 |
if (fusion.left == 6994359 && fusion.right == 17581683) |
| 750 |
{ |
| 751 |
const char* dir_str = "ff"; |
| 752 |
if (dir == FUSION_FR) |
| 753 |
dir_str = "fr"; |
| 754 |
else if (dir == FUSION_RF) |
| 755 |
dir_str = "rf"; |
| 756 |
else if (dir == FUSION_RR) |
| 757 |
dir_str = "rr"; |
| 758 |
|
| 759 |
cout << "paired-end from two chromosomes" << endl; |
| 760 |
cout << "insert id: " << lh.insert_id() << endl; |
| 761 |
cout << dir_str << " : " << (lh.antisense_align() ? "-" : "+") << " " << (rh.antisense_align() ? "-" : "+") << endl; |
| 762 |
cout << lh.ref_id() << ": " << lh.left() << "-" << lh.right() << endl; |
| 763 |
cout << lh.ref_id2() << " " << print_cigar(lh.cigar()) << endl; |
| 764 |
cout << rh.ref_id() << ": " << rh.left() << "-" << rh.right() << endl; |
| 765 |
cout << rh.ref_id2() << " " << print_cigar(rh.cigar()) << endl; |
| 766 |
cout << "left: " << left1 << "-" << left2 << endl; |
| 767 |
cout << "right: " << right1 << "-" << right2 << endl; |
| 768 |
cout << endl; |
| 769 |
} |
| 770 |
#endif |
| 771 |
|
| 772 |
if (ref_id1 > ref_id2 || (ref_id1 == ref_id2 && lh.left() > rh.left())) |
| 773 |
{ |
| 774 |
uint32_t temp = ref_id1; |
| 775 |
ref_id1 = ref_id2; |
| 776 |
ref_id2 = temp; |
| 777 |
|
| 778 |
temp = left1; |
| 779 |
left1 = right1; |
| 780 |
right1 = temp; |
| 781 |
|
| 782 |
temp = left2; |
| 783 |
left2 = right2; |
| 784 |
right2 = temp; |
| 785 |
} |
| 786 |
|
| 787 |
lb = fusions_ref.upper_bound(Fusion(ref_id1, ref_id2, left1, right1)); |
| 788 |
ub = fusions_ref.lower_bound(Fusion(ref_id1, ref_id2, left2, right2)); |
| 789 |
|
| 790 |
// daehwan |
| 791 |
#if 0 |
| 792 |
static const uint32_t chr_id1 = RefSequenceTable::hash_string("chr2"); |
| 793 |
static const uint32_t chr_id2 = RefSequenceTable::hash_string("chr3"); |
| 794 |
|
| 795 |
if ((lh.ref_id() == chr_id1 && rh.ref_id() == chr_id2) || |
| 796 |
(lh.ref_id() == chr_id2 && rh.ref_id() == chr_id1)) |
| 797 |
{ |
| 798 |
// KPL-4 BSG 19:571325-583492:1 NFIX 19:13106584-13209610:1 |
| 799 |
// const uint32_t left1 = 571325, right1 = 583492, left2 = 13106584, right2 = 13209610; |
| 800 |
|
| 801 |
// SK-BR-3 DHX35 20:37590942-37668366:1 ITCH 20:32951041-33099198:1 |
| 802 |
// const uint32_t left1 = 37590942, right1 = 37668366, left2 = 32951041, right2 = 33099198; |
| 803 |
|
| 804 |
// SK-BR-3 NFS1 20:34220262-34287287:-1 PREX1 20:47240790-47444420:-1 |
| 805 |
// const uint32_t left1 = 34220262, right1 = 34287287, left2 = 47240790, right2 = 47444420; |
| 806 |
|
| 807 |
// VCaP TIA1 2:70436576-70475792:-1 DIRC2 3:122513642-122599986:1 |
| 808 |
uint32_t left1 = 70436576, right1 = 70475792, left2 = 122513642, right2 = 122599986; |
| 809 |
if (lh.ref_id() != chr_id1) |
| 810 |
{ |
| 811 |
uint32_t temp = left1; |
| 812 |
left1 = left2; |
| 813 |
left2 = temp; |
| 814 |
|
| 815 |
temp = right1; |
| 816 |
right1 = right2; |
| 817 |
right2 = temp; |
| 818 |
} |
| 819 |
|
| 820 |
if ((lh.left() >= left1 && lh.left() <= right1 && rh.left() >= left2 && rh.left() <= right2) || |
| 821 |
(lh.left() >= left2 && lh.left() <= right2 && rh.left() >= left1 && rh.left() <= right1)) |
| 822 |
{ |
| 823 |
for (size_t t = 0; t < left.size(); ++t) |
| 824 |
{ |
| 825 |
const BowtieHit& lh = left[t]; |
| 826 |
const BowtieHit& rh = right[t]; |
| 827 |
|
| 828 |
const char* dir_str = "ff"; |
| 829 |
if (dir == FUSION_FR) |
| 830 |
dir_str = "fr"; |
| 831 |
else if (dir == FUSION_RF) |
| 832 |
dir_str = "rf"; |
| 833 |
else if (dir == FUSION_RR) |
| 834 |
dir_str = "rr"; |
| 835 |
|
| 836 |
cout << "paired-end from two chromosomes" << endl; |
| 837 |
cout << "insert id: " << lh.insert_id() << endl; |
| 838 |
cout << dir_str << " : " << (lh.antisense_align() ? "-" : "+") << " " << (rh.antisense_align() ? "-" : "+") << endl; |
| 839 |
cout << lh.ref_id() << ": " << lh.left() << "-" << lh.right() << endl; |
| 840 |
cout << lh.ref_id2() << " " << print_cigar(lh.cigar()) << endl; |
| 841 |
cout << rh.ref_id() << ": " << rh.left() << "-" << rh.right() << endl; |
| 842 |
cout << rh.ref_id2() << " " << print_cigar(rh.cigar()) << endl; |
| 843 |
cout << "left: " << left1 << "-" << left2 << endl; |
| 844 |
cout << "right: " << right1 << "-" << right2 << endl; |
| 845 |
cout << endl; |
| 846 |
} |
| 847 |
} |
| 848 |
} |
| 849 |
#endif |
| 850 |
} |
| 851 |
|
| 852 |
while (lb != ub && lb != fusions_ref.end()) |
| 853 |
{ |
| 854 |
if (lb->first.dir == dir && |
| 855 |
lb->first.refid1 == ref_id1 && |
| 856 |
lb->first.refid2 == ref_id2 && |
| 857 |
((!fusionSpanned && lb->first.right >= right1 && lb->first.right <= right2) || fusionSpanned) && |
| 858 |
!lb->second.reversed) |
| 859 |
{ |
| 860 |
int dist = 0, left_dist = 0, right_dist = 0; |
| 861 |
|
| 862 |
// daehwan - check this out |
| 863 |
if (!fusionSpanned || fusion_leftSide) |
| 864 |
{ |
| 865 |
if (dir == FUSION_RF || dir == FUSION_RR) |
| 866 |
left_dist = (left2 - inner_dist) - (int)lb->first.left; |
| 867 |
else |
| 868 |
left_dist = (int)lb->first.left - (left1 + inner_dist); |
| 869 |
} |
| 870 |
|
| 871 |
if (!fusionSpanned || !fusion_leftSide) |
| 872 |
{ |
| 873 |
if (dir == FUSION_FR || dir == FUSION_RR) |
| 874 |
right_dist = (int)lb->first.right - (right1 + inner_dist); |
| 875 |
else |
| 876 |
right_dist = (right2 - inner_dist) - (int)lb->first.right; |
| 877 |
} |
| 878 |
|
| 879 |
dist = abs(left_dist) + abs(right_dist); |
| 880 |
|
| 881 |
// daehwan - fix this later |
| 882 |
if (dist < 0 && fusionSpanned) |
| 883 |
unsupport = true; |
| 884 |
bool pass = dist < max_dist; |
| 885 |
|
| 886 |
// daehwan |
| 887 |
#if 0 |
| 888 |
// if(!fusionSpanned) |
| 889 |
// if (pass && !unsupport) |
| 890 |
if (lb->first.left == 6994359 && lb->first.right == 17581683) |
| 891 |
{ |
| 892 |
const char* dir_str = "ff"; |
| 893 |
if (dir == FUSION_FR) |
| 894 |
dir_str = "fr"; |
| 895 |
else if (dir == FUSION_RF) |
| 896 |
dir_str = "rf"; |
| 897 |
else if (dir == FUSION_RR) |
| 898 |
dir_str = "rr"; |
| 899 |
|
| 900 |
cout << dir_str << endl; |
| 901 |
cout << "dist: " << dist << endl; |
| 902 |
cout << lb->first.refid1 << " " << lb->first.refid2 << endl; |
| 903 |
cout << lb->first.left << "-" << lb->first.right << endl; |
| 904 |
cout << "unsupport: " << (unsupport ? "yes" : "no") << endl; |
| 905 |
cout << "pass: " << (pass ? "yes" : "no") << endl; |
| 906 |
cout << "ids: " << lh.insert_id() << " : " << rh.insert_id() << endl; |
| 907 |
cout << endl << endl; |
| 908 |
} |
| 909 |
#endif |
| 910 |
|
| 911 |
FusionSet::iterator itr = fusions.find(lb->first); |
| 912 |
if (itr != fusions.end()) |
| 913 |
{ |
| 914 |
if (unsupport) |
| 915 |
++(itr->second.unsupport_count_pair); |
| 916 |
else if (pass) |
| 917 |
{ |
| 918 |
if (fusionSpanned) |
| 919 |
++(itr->second.pair_count_fusion); |
| 920 |
else |
| 921 |
{ |
| 922 |
itr->second.vPairSupport.push_back(FusionPairSupport(left_dist, right_dist)); |
| 923 |
++(itr->second.pair_count); |
| 924 |
|
| 925 |
if (itr->second.vPairSupport.size() >= 300) |
| 926 |
{ |
| 927 |
sort(itr->second.vPairSupport.begin(), itr->second.vPairSupport.end()); |
| 928 |
itr->second.vPairSupport.erase(itr->second.vPairSupport.begin() + 200, itr->second.vPairSupport.end()); |
| 929 |
} |
| 930 |
} |
| 931 |
} |
| 932 |
} |
| 933 |
else |
| 934 |
{ |
| 935 |
FusionStat fusionStat; |
| 936 |
if (unsupport) |
| 937 |
fusionStat.unsupport_count_pair = 1; |
| 938 |
else if (pass) |
| 939 |
{ |
| 940 |
if (fusionSpanned) |
| 941 |
fusionStat.pair_count_fusion = 1; |
| 942 |
else |
| 943 |
{ |
| 944 |
fusionStat.vPairSupport.push_back(FusionPairSupport(left_dist, right_dist)); |
| 945 |
fusionStat.pair_count = 1; |
| 946 |
} |
| 947 |
} |
| 948 |
|
| 949 |
fusions[lb->first] = fusionStat; |
| 950 |
} |
| 951 |
} |
| 952 |
|
| 953 |
if (fusionSpanned) |
| 954 |
break; |
| 955 |
|
| 956 |
++lb; |
| 957 |
} |
| 958 |
} |
| 959 |
} |
| 960 |
|
| 961 |
void merge_with(FusionSimpleSet& fusions, const FusionSimpleSet& other_fusions) |
| 962 |
{ |
| 963 |
for (FusionSimpleSet::const_iterator other_itr = other_fusions.begin(); other_itr != other_fusions.end(); ++other_itr) |
| 964 |
{ |
| 965 |
FusionSimpleSet::iterator itr = fusions.find(other_itr->first); |
| 966 |
if (itr != fusions.end()) |
| 967 |
{ |
| 968 |
FusionSimpleStat& curr = itr->second; |
| 969 |
curr.merge_with(other_itr->second); |
| 970 |
} |
| 971 |
else |
| 972 |
{ |
| 973 |
fusions[other_itr->first] = other_itr->second; |
| 974 |
} |
| 975 |
} |
| 976 |
} |
| 977 |
|
| 978 |
void merge_with(FusionSet& fusions, const FusionSet& other_fusions) |
| 979 |
{ |
| 980 |
for (FusionSet::const_iterator other_itr = other_fusions.begin(); other_itr != other_fusions.end(); ++other_itr) |
| 981 |
{ |
| 982 |
FusionSet::iterator itr = fusions.find(other_itr->first); |
| 983 |
if (itr != fusions.end()) |
| 984 |
{ |
| 985 |
FusionStat& curr = itr->second; |
| 986 |
curr.merge_with(other_itr->second); |
| 987 |
} |
| 988 |
else |
| 989 |
{ |
| 990 |
fusions[other_itr->first] = other_itr->second; |
| 991 |
} |
| 992 |
} |
| 993 |
} |
