|
1
|
1 /*
|
|
|
2 * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
|
|
|
3 * All rights reserved.
|
|
|
4 *
|
|
|
5 * Redistribution and use in source and binary forms, with or without modification,
|
|
|
6 * are permitted provided that the following conditions are met:
|
|
|
7 *
|
|
|
8 * Redistributions of source code must retain the above copyright notice, this list
|
|
|
9 * of conditions and the following disclaimer.
|
|
|
10 * - Redistributions in binary form must reproduce the above copyright notice, this
|
|
|
11 * list of conditions and the following disclaimer in the documentation and/or other
|
|
|
12 * materials provided with the distribution.
|
|
|
13 * - Neither the names of the University of Washington, Simon Fraser University,
|
|
|
14 * nor the names of its contributors may be
|
|
|
15 * used to endorse or promote products derived from this software without specific
|
|
|
16 * prior written permission.
|
|
|
17 *
|
|
|
18 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
|
|
|
19 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
|
|
|
20 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
|
|
|
21 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
|
|
|
22 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
|
|
|
23 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
|
|
|
24 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
|
|
|
25 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
|
|
|
26 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
|
|
|
27 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
|
|
28 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
|
|
29 */
|
|
|
30
|
|
|
31 /*
|
|
|
32 Authors:
|
|
|
33 Farhad Hormozdiari
|
|
|
34 Faraz Hach
|
|
|
35 Can Alkan
|
|
|
36 Emails:
|
|
|
37 farhadh AT uw DOT edu
|
|
|
38 fhach AT cs DOT sfu DOT ca
|
|
|
39 calkan AT uw DOT edu
|
|
|
40 */
|
|
|
41
|
|
|
42
|
|
|
43
|
|
|
44
|
|
|
45
|
|
|
46 #include <stdio.h>
|
|
|
47 #include <stdlib.h>
|
|
|
48 #include <string.h>
|
|
|
49 #include <math.h>
|
|
|
50 #include "Common.h"
|
|
|
51 #include "CommandLineParser.h"
|
|
|
52 #include "Reads.h"
|
|
|
53 #include "Output.h"
|
|
|
54 #include "HashTable.h"
|
|
|
55 #include "MrFAST.h"
|
|
|
56
|
|
|
57 char *versionNumber = "2.1"; // Current Version
|
|
|
58 unsigned char seqFastq;
|
|
|
59
|
|
|
60 int main(int argc, char *argv[])
|
|
|
61 {
|
|
|
62 if (!parseCommandLine(argc, argv))
|
|
|
63 return 1;
|
|
|
64
|
|
|
65 configHashTable();
|
|
|
66 /****************************************************
|
|
|
67 * INDEXING
|
|
|
68 ***************************************************/
|
|
|
69 if (indexingMode)
|
|
|
70 {
|
|
|
71 int i;
|
|
|
72 /********************************
|
|
|
73 * Regular Mode
|
|
|
74 ********************************/
|
|
|
75 configHashTable();
|
|
|
76 for (i = 0; i < fileCnt; i++)
|
|
|
77 {
|
|
|
78 generateHashTable(fileName[i][0], fileName[i][1]);
|
|
|
79 }
|
|
|
80 }
|
|
|
81 /****************************************************
|
|
|
82 * SEARCHING
|
|
|
83 ***************************************************/
|
|
|
84 else
|
|
|
85 {
|
|
|
86 Read *seqList;
|
|
|
87 unsigned int seqListSize;
|
|
|
88 int fc;
|
|
|
89 int samplingLocsSize;
|
|
|
90 int *samplingLocs;
|
|
|
91 double totalLoadingTime = 0;
|
|
|
92 double totalMappingTime = 0;
|
|
|
93 double startTime;
|
|
|
94 double loadingTime;
|
|
|
95 double mappingTime;
|
|
|
96 double lstartTime;
|
|
|
97 double ppTime = 0.0;
|
|
|
98 double tmpTime;;
|
|
|
99 char *prevGen = getMem(CONTIG_NAME_SIZE);
|
|
|
100 prevGen[0]='\0';
|
|
|
101 char *curGen;
|
|
|
102 int flag;
|
|
|
103 double maxMem=0;
|
|
|
104 char fname1[FILE_NAME_LENGTH];
|
|
|
105 char fname2[FILE_NAME_LENGTH];
|
|
|
106 char fname3[FILE_NAME_LENGTH];
|
|
|
107 char fname4[FILE_NAME_LENGTH];
|
|
|
108 char fname5[FILE_NAME_LENGTH];
|
|
|
109
|
|
|
110 char outputFileName[FILE_NAME_LENGTH];
|
|
|
111 // Loading Sequences & Sampling Locations
|
|
|
112 startTime = getTime();
|
|
|
113 if (!readAllReads(seqFile1, seqFile2, seqCompressed, &seqFastq, pairedEndMode, &seqList, &seqListSize))
|
|
|
114 {
|
|
|
115 return 1;
|
|
|
116 }
|
|
|
117
|
|
|
118 loadSamplingLocations(&samplingLocs, &samplingLocsSize);
|
|
|
119 totalLoadingTime += getTime()-startTime;
|
|
|
120
|
|
|
121 if (pairedEndMode)
|
|
|
122 {
|
|
|
123 //Switching to Inferred Size
|
|
|
124 minPairEndedDistance = minPairEndedDistance - SEQ_LENGTH + 2;
|
|
|
125 maxPairEndedDistance = maxPairEndedDistance - SEQ_LENGTH + 2;
|
|
|
126 if (pairedEndDiscordantMode)
|
|
|
127 {
|
|
|
128 maxPairEndedDiscordantDistance = maxPairEndedDiscordantDistance - SEQ_LENGTH + 2;
|
|
|
129 minPairEndedDiscordantDistance = minPairEndedDiscordantDistance - SEQ_LENGTH + 2;
|
|
|
130 }
|
|
|
131
|
|
|
132 sprintf(fname1, "__%s__1", mappingOutput);
|
|
|
133 sprintf(fname2, "__%s__2", mappingOutput);
|
|
|
134 sprintf(fname3, "__%s__disc", mappingOutput);
|
|
|
135 sprintf(fname4, "__%s__oea1", mappingOutput);
|
|
|
136 sprintf(fname5, "__%s__oea2", mappingOutput);
|
|
|
137 unlink(fname1);
|
|
|
138 unlink(fname2);
|
|
|
139 unlink(fname3);
|
|
|
140 unlink(fname4);
|
|
|
141 unlink(fname5);
|
|
|
142 }
|
|
|
143
|
|
|
144 sprintf(outputFileName, "%s%s",mappingOutputPath , mappingOutput);
|
|
|
145 // Preparing output
|
|
|
146 initOutput(outputFileName, outCompressed);
|
|
|
147
|
|
|
148 fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
|
|
|
149 fprintf(stdout, "| %15s | %15s | %15s | %15s | %15s %15s |\n","Genome Name","Loading Time", "Mapping Time", "Memory Usage(M)","Total Mappings","Mapped reads");
|
|
|
150 fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
|
|
|
151
|
|
|
152 /********************************
|
|
|
153 * Regular Mode
|
|
|
154 ********************************/
|
|
|
155 if (!pairedEndMode)
|
|
|
156 {
|
|
|
157 initLookUpTable();
|
|
|
158 if(bestMode)
|
|
|
159 initBestMapping(seqListSize);
|
|
|
160
|
|
|
161 for (fc = 0; fc <fileCnt; fc++)
|
|
|
162 {
|
|
|
163 if (!initLoadingHashTable(fileName[fc][1]))
|
|
|
164 {
|
|
|
165 return 1;
|
|
|
166 }
|
|
|
167
|
|
|
168 mappingTime = 0;
|
|
|
169 loadingTime = 0;
|
|
|
170 prevGen[0] = '\0';
|
|
|
171 flag = 1;
|
|
|
172
|
|
|
173 do
|
|
|
174 {
|
|
|
175 flag = loadHashTable ( &tmpTime, errThreshold); // Reading a fragment
|
|
|
176 curGen = getRefGenomeName();
|
|
|
177
|
|
|
178 // First Time
|
|
|
179 if (flag && prevGen[0]== '\0')
|
|
|
180 {
|
|
|
181 sprintf(prevGen, "%s", curGen);
|
|
|
182 }
|
|
|
183
|
|
|
184 if ( !flag || strcmp(prevGen, curGen)!=0)
|
|
|
185 {
|
|
|
186
|
|
|
187 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
|
|
|
188 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
|
|
|
189 fflush(stdout);
|
|
|
190
|
|
|
191 totalMappingTime += mappingTime;
|
|
|
192 totalLoadingTime += loadingTime;
|
|
|
193
|
|
|
194 loadingTime = 0;
|
|
|
195 mappingTime = 0;
|
|
|
196 maxMem = 0;
|
|
|
197
|
|
|
198 if (!flag)
|
|
|
199 {
|
|
|
200 break;
|
|
|
201 }
|
|
|
202 }
|
|
|
203 else if (progressRep && mappingTime != 0)
|
|
|
204 {
|
|
|
205 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
|
|
|
206 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
|
|
|
207 fflush(stdout);
|
|
|
208 }
|
|
|
209
|
|
|
210 sprintf(prevGen, "%s", curGen);
|
|
|
211
|
|
|
212 loadingTime += tmpTime;
|
|
|
213 // lstartTime = getTime();
|
|
|
214
|
|
|
215 initFAST(seqList, seqListSize, samplingLocs, samplingLocsSize, fileName[fc][0]);
|
|
|
216
|
|
|
217 lstartTime = getTime();
|
|
|
218
|
|
|
219
|
|
|
220 mapAllSingleEndSeq();
|
|
|
221
|
|
|
222
|
|
|
223
|
|
|
224 mappingTime += getTime() - lstartTime;
|
|
|
225 if (maxMem < getMemUsage())
|
|
|
226 {
|
|
|
227 maxMem = getMemUsage();
|
|
|
228 }
|
|
|
229 } while (flag);
|
|
|
230
|
|
|
231 } // end for;
|
|
|
232 if(bestMode)
|
|
|
233 finalizeBestSingleMapping();
|
|
|
234 finalizeFAST();
|
|
|
235 finalizeLoadingHashTable();
|
|
|
236
|
|
|
237 }
|
|
|
238 // Pairedend Mapping Mode
|
|
|
239 else
|
|
|
240 {
|
|
|
241 initLookUpTable();
|
|
|
242 if(pairedEndMode)
|
|
|
243 initBestConcordantDiscordant(seqListSize);
|
|
|
244 for (fc = 0; fc < fileCnt; fc++)
|
|
|
245 {
|
|
|
246 if (!initLoadingHashTable(fileName[fc][1]))
|
|
|
247 {
|
|
|
248 return 1;
|
|
|
249 }
|
|
|
250 mappingTime = 0;
|
|
|
251 loadingTime = 0;
|
|
|
252 prevGen[0] = '\0';
|
|
|
253 flag = 1;
|
|
|
254
|
|
|
255 do
|
|
|
256 {
|
|
|
257 flag = loadHashTable ( &tmpTime , errThreshold); // Reading a fragment
|
|
|
258 curGen = getRefGenomeName();
|
|
|
259
|
|
|
260 // First Time
|
|
|
261 if (flag && prevGen[0]== '\0')
|
|
|
262 {
|
|
|
263 sprintf(prevGen, "%s", curGen);
|
|
|
264 }
|
|
|
265
|
|
|
266 if ( !flag || strcmp(prevGen, curGen)!=0)
|
|
|
267 {
|
|
|
268
|
|
|
269 // DISCORDANT
|
|
|
270 lstartTime = getTime();
|
|
|
271 outputPairedEnd();
|
|
|
272 mappingTime += getTime() - lstartTime;
|
|
|
273 //DISCORDANT
|
|
|
274
|
|
|
275 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
|
|
|
276 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
|
|
|
277 fflush(stdout);
|
|
|
278
|
|
|
279 totalMappingTime += mappingTime;
|
|
|
280 totalLoadingTime += loadingTime;
|
|
|
281
|
|
|
282 loadingTime = 0;
|
|
|
283 mappingTime = 0;
|
|
|
284 maxMem = 0;
|
|
|
285
|
|
|
286 if (!flag)
|
|
|
287 {
|
|
|
288 break;
|
|
|
289 }
|
|
|
290 }
|
|
|
291 else if (progressRep && mappingTime != 0)
|
|
|
292 {
|
|
|
293 fprintf(stdout, "| %15s | %15.2f | %15.2f | %15.2f | %15lld %15lld |\n",
|
|
|
294 prevGen,loadingTime, mappingTime, maxMem, mappingCnt , mappedSeqCnt);
|
|
|
295 fflush(stdout);
|
|
|
296 }
|
|
|
297
|
|
|
298 sprintf(prevGen, "%s", curGen);
|
|
|
299
|
|
|
300 loadingTime += tmpTime;
|
|
|
301 lstartTime = getTime();
|
|
|
302
|
|
|
303 initFAST(seqList, seqListSize, samplingLocs, samplingLocsSize, fileName[fc][0]);
|
|
|
304
|
|
|
305 mapPairedEndSeq();
|
|
|
306
|
|
|
307 mappingTime += getTime() - lstartTime;
|
|
|
308 if (maxMem < getMemUsage())
|
|
|
309 {
|
|
|
310 maxMem = getMemUsage();
|
|
|
311 }
|
|
|
312
|
|
|
313 } while (flag);
|
|
|
314
|
|
|
315 } // end for;
|
|
|
316
|
|
|
317 if(pairedEndMode)
|
|
|
318 {
|
|
|
319 sprintf(outputFileName, "%s%s",mappingOutputPath , mappingOutput);
|
|
|
320 finalizeOEAReads(outputFileName);
|
|
|
321 outputAllTransChromosal(transChromosal);
|
|
|
322 finalizeBestConcordantDiscordant();
|
|
|
323 }
|
|
|
324
|
|
|
325 finalizeLoadingHashTable();
|
|
|
326
|
|
|
327 if (pairedEndDiscordantMode)
|
|
|
328 {
|
|
|
329 lstartTime = getTime();
|
|
|
330 outputPairedEndDiscPP();
|
|
|
331 ppTime = getTime() - lstartTime;
|
|
|
332 }
|
|
|
333 finalizeFAST();
|
|
|
334 } //else
|
|
|
335
|
|
|
336 finalizeOutput();
|
|
|
337
|
|
|
338 fprintf(stdout, "-----------------------------------------------------------------------------------------------------------\n");
|
|
|
339 fprintf(stdout, "%19s%16.2f%18.2f\n\n", "Total:",totalLoadingTime, totalMappingTime);
|
|
|
340 if (pairedEndDiscordantMode)
|
|
|
341 fprintf(stdout, "Post Processing Time: %18.2f \n", ppTime);
|
|
|
342 fprintf(stdout, "%-30s%10.2f\n","Total Time:", totalMappingTime+totalLoadingTime);
|
|
|
343 fprintf(stdout, "%-30s%10d\n","Total No. of Reads:", seqListSize);
|
|
|
344 fprintf(stdout, "%-30s%10lld\n","Total No. of Mappings:", mappingCnt);
|
|
|
345 fprintf(stdout, "%-30s%10.0f\n\n","Avg No. of locations verified:", ceil((float)verificationCnt/seqListSize));
|
|
|
346
|
|
|
347 int cof = (pairedEndMode)?2:1;
|
|
|
348
|
|
|
349 if (progressRep && maxHits != 0)
|
|
|
350 {
|
|
|
351 int frequency[maxHits+1];
|
|
|
352 int i;
|
|
|
353 for ( i=0 ; i <= maxHits; i++)
|
|
|
354 {
|
|
|
355 frequency[i] = 0;
|
|
|
356 }
|
|
|
357
|
|
|
358
|
|
|
359 for (fc = 0; fc < seqListSize; fc++)
|
|
|
360 {
|
|
|
361 frequency[(int)(*(seqList[fc*cof].hits))]++;
|
|
|
362 }
|
|
|
363 frequency[maxHits] = completedSeqCnt;
|
|
|
364 for ( i=0 ; i <= maxHits; i++)
|
|
|
365 {
|
|
|
366 fprintf(stdout, "%-30s%10d%10d%10.2f%%\n","Reads Mapped to ", i, frequency[i], 100*(float)frequency[i]/(float)seqListSize);
|
|
|
367 }
|
|
|
368 }
|
|
|
369
|
|
|
370
|
|
|
371 finalizeReads(unmappedOutput);
|
|
|
372 freeMem(prevGen, CONTIG_NAME_SIZE);
|
|
|
373 }
|
|
|
374
|
|
|
375 return 1;
|
|
|
376 }
|
