0
|
1 #include <stdio.h>
|
|
2 #include <getopt.h>
|
|
3 #include <vector>
|
|
4 #include <pthread.h>
|
|
5
|
|
6 #include "alignments.hpp"
|
|
7 #include "SubexonGraph.hpp"
|
|
8 #include "SubexonCorrelation.hpp"
|
|
9 #include "Constraints.hpp"
|
|
10 #include "TranscriptDecider.hpp"
|
|
11
|
|
12 char usage[] = "./classes [OPTIONS]:\n"
|
|
13 "Required:\n"
|
|
14 "\t-s STRING: path to the subexon file.\n"
|
|
15 "\t-b STRING: path to the BAM file.\n"
|
|
16 "\t\tor\n"
|
|
17 "\t--lb STRING: path to the file of the list of BAM files.\n"
|
|
18 "Optional:\n"
|
|
19 "\t-p INT: number of threads. (default: 1)\n"
|
|
20 "\t-o STRING: the prefix of the output file. (default: not used)\n"
|
|
21 "\t-c FLOAT: only use the subexons with classifier score <= than the given number. (default: 0.05)\n"
|
|
22 "\t-f FLOAT: filter the transcript from the gene if its abundance is lower than the given number percent of the most abundant one. (default: 0.05)\n"
|
|
23 "\t-d FLOAT: filter the transcript whose average read depth is less than the given number. (default: 2.5)\n"
|
|
24 "\t--ls STRING: path to the file of the list of single-sample subexon files. (default: not used)\n"
|
|
25 "\t--hasMateIdSuffix: the read id has suffix such as .1, .2 for a mate pair. (default: false)\n"
|
|
26 "\t--maxDpConstraintSize: the maximum number of subexons a constraint can cover in dynamic programming. (default: 7; -1 for inf)\n"
|
|
27 "\t--primaryParalog: use primary alignment to retain paralog genes instead of unique alignments. (default: not used)\n"
|
|
28 ;
|
|
29
|
|
30 static const char *short_options = "s:b:f:o:d:p:c:h" ;
|
|
31 static struct option long_options[] =
|
|
32 {
|
|
33 { "ls", required_argument, 0, 10000 },
|
|
34 { "lb", required_argument, 0, 10001 },
|
|
35 { "hasMateIdSuffix", no_argument, 0, 10002 },
|
|
36 { "primaryParalog", no_argument, 0, 10003 },
|
|
37 { "maxDpConstraintSize", required_argument, 0, 10004 },
|
|
38 { (char *)0, 0, 0, 0}
|
|
39 } ;
|
|
40
|
|
41 struct _getAlignmentsInfoThreadArg
|
|
42 {
|
|
43 std::vector<Alignments> *pAlignmentFiles ;
|
|
44 int numThreads ;
|
|
45 int tid ;
|
|
46 } ;
|
|
47
|
|
48 struct _getConstraintsThreadArg
|
|
49 {
|
|
50 std::vector<Constraints> *pMultiSampleConstraints ;
|
|
51 int numThreads ;
|
|
52 int tid ;
|
|
53
|
|
54 struct _subexon *subexons ;
|
|
55 int seCnt ;
|
|
56 int start, end ;
|
|
57 } ;
|
|
58
|
|
59 void *GetAlignmentsInfo_Thread( void *pArg )
|
|
60 {
|
|
61 int i ;
|
|
62 std::vector <Alignments> &alignmentFiles = *( ( (struct _getAlignmentsInfoThreadArg *)pArg )->pAlignmentFiles ) ;
|
|
63 int tid = ( (struct _getAlignmentsInfoThreadArg *)pArg )->tid ;
|
|
64 int numThreads = ( (struct _getAlignmentsInfoThreadArg *)pArg )->numThreads ;
|
|
65 int size = alignmentFiles.size() ;
|
|
66 for ( i = 0 ; i < size ; ++i )
|
|
67 {
|
|
68 if ( i % numThreads == tid )
|
|
69 {
|
|
70 alignmentFiles[i].GetGeneralInfo( true ) ;
|
|
71 alignmentFiles[i].Rewind() ;
|
|
72 }
|
|
73 }
|
|
74
|
|
75 pthread_exit( NULL ) ;
|
|
76 }
|
|
77
|
|
78
|
|
79 void *GetConstraints_Thread( void *pArg )
|
|
80 {
|
|
81 int i ;
|
|
82 struct _getConstraintsThreadArg &arg = *( (struct _getConstraintsThreadArg *)pArg ) ;
|
|
83 std::vector<Constraints> &multiSampleConstraints = *( arg.pMultiSampleConstraints ) ;
|
|
84 int tid = arg.tid ;
|
|
85 int numThreads = arg.numThreads ;
|
|
86 int size = multiSampleConstraints.size() ;
|
|
87 for ( i = 0 ; i < size ; ++i )
|
|
88 {
|
|
89 if ( i % numThreads == tid )
|
|
90 multiSampleConstraints[i].BuildConstraints( arg.subexons, arg.seCnt, arg.start, arg.end ) ;
|
|
91 }
|
|
92 pthread_exit( NULL ) ;
|
|
93 }
|
|
94
|
|
95 int main( int argc, char *argv[] )
|
|
96 {
|
|
97 int i, j ;
|
|
98 int size ;
|
|
99
|
|
100 if ( argc <= 1 )
|
|
101 {
|
|
102 printf( "%s", usage ) ;
|
|
103 return 0 ;
|
|
104 }
|
|
105
|
|
106 int c, option_index ; // For getopt
|
|
107 option_index = 0 ;
|
|
108 FILE *fpSubexon = NULL ;
|
|
109 double FPKMFraction = 0.05 ;
|
|
110 double classifierThreshold ;
|
|
111 double txptMinReadDepth = 2.5 ;
|
|
112 char outputPrefix[1024] = "" ;
|
|
113 int numThreads = 1 ;
|
|
114 bool hasMateReadIdSuffix = false ;
|
|
115 bool usePrimaryAsUnique = false ;
|
|
116 int maxDpConstraintSize = 7 ;
|
|
117
|
|
118 std::vector<Alignments> alignmentFiles ;
|
|
119 SubexonCorrelation subexonCorrelation ;
|
|
120
|
|
121 classifierThreshold = 0.05 ;
|
|
122 while ( 1 )
|
|
123 {
|
|
124 c = getopt_long( argc, argv, short_options, long_options, &option_index ) ;
|
|
125 if ( c == -1 )
|
|
126 break ;
|
|
127
|
|
128 if ( c == 's' )
|
|
129 {
|
|
130 fpSubexon = fopen( optarg, "r" ) ;
|
|
131 }
|
|
132 else if ( c == 'b' )
|
|
133 {
|
|
134 Alignments a ;
|
|
135 a.Open( optarg ) ;
|
|
136 //a.SetAllowClip( false ) ;
|
|
137 alignmentFiles.push_back( a ) ;
|
|
138 }
|
|
139 else if ( c == 'c' )
|
|
140 {
|
|
141 classifierThreshold = atof( optarg ) ;
|
|
142 }
|
|
143 else if ( c == 'f' )
|
|
144 {
|
|
145 FPKMFraction = atof( optarg ) ;
|
|
146 }
|
|
147 else if ( c == 'o' )
|
|
148 {
|
|
149 strcpy( outputPrefix, optarg ) ;
|
|
150 }
|
|
151 else if ( c == 'd' )
|
|
152 {
|
|
153 txptMinReadDepth = atof( optarg ) ;
|
|
154 }
|
|
155 else if ( c == 'p' )
|
|
156 {
|
|
157 numThreads = atoi( optarg ) ;
|
|
158 }
|
|
159 else if ( c == 10000 ) // the list of subexon files.
|
|
160 {
|
|
161 subexonCorrelation.Initialize( optarg ) ;
|
|
162 }
|
|
163 else if ( c == 10001 ) // the list of bam files.
|
|
164 {
|
|
165 FILE *fp = fopen( optarg, "r" ) ;
|
|
166 char buffer[1024] ;
|
|
167 while ( fgets( buffer, sizeof( buffer ), fp ) != NULL )
|
|
168 {
|
|
169 int len = strlen( buffer ) ;
|
|
170 if ( buffer[len - 1] == '\n' )
|
|
171 {
|
|
172 buffer[len - 1] = '\0' ;
|
|
173 --len ;
|
|
174
|
|
175 }
|
|
176 Alignments a ;
|
|
177 a.Open( buffer ) ;
|
|
178 alignmentFiles.push_back( a ) ;
|
|
179 }
|
|
180 fclose( fp ) ;
|
|
181 }
|
|
182 else if ( c == 10002 ) // the mate pair read id has suffix.
|
|
183 {
|
|
184 hasMateReadIdSuffix = true ;
|
|
185 }
|
|
186 else if ( c == 10003 ) // do not check unique alignment
|
|
187 {
|
|
188 usePrimaryAsUnique = true ;
|
|
189 }
|
|
190 else if ( c == 10004 ) // maxDpConstraintSize
|
|
191 {
|
|
192 maxDpConstraintSize = atoi(optarg) ;
|
|
193 }
|
|
194 else
|
|
195 {
|
|
196 printf( "%s", usage ) ;
|
|
197 exit( 1 ) ;
|
|
198 }
|
|
199 }
|
|
200 if ( fpSubexon == NULL )
|
|
201 {
|
|
202 printf( "Cannot find combined subexon file.\n" ) ;
|
|
203 exit( 1 ) ;
|
|
204 }
|
|
205 if ( alignmentFiles.size() < 1 )
|
|
206 {
|
|
207 printf( "Must use -b option to specify BAM files.\n" ) ;
|
|
208 exit( 1 ) ;
|
|
209 }
|
|
210
|
|
211
|
|
212 if ( alignmentFiles.size() < 50 )
|
|
213 {
|
|
214 size = alignmentFiles.size() ;
|
|
215 for ( i = 0 ; i < size ; ++i )
|
|
216 {
|
|
217 alignmentFiles[i].GetGeneralInfo( true ) ;
|
|
218 alignmentFiles[i].Rewind() ;
|
|
219 }
|
|
220 }
|
|
221 else
|
|
222 {
|
|
223 struct _getAlignmentsInfoThreadArg *args = new struct _getAlignmentsInfoThreadArg[ numThreads ] ;
|
|
224 pthread_attr_t pthreadAttr ;
|
|
225 pthread_t *threads ;
|
|
226
|
|
227 pthread_attr_init( &pthreadAttr ) ;
|
|
228 pthread_attr_setdetachstate( &pthreadAttr, PTHREAD_CREATE_JOINABLE ) ;
|
|
229
|
|
230 threads = new pthread_t[ numThreads ] ;
|
|
231
|
|
232 for ( i = 0 ; i < numThreads ; ++i )
|
|
233 {
|
|
234 args[i].pAlignmentFiles = &alignmentFiles ;
|
|
235 args[i].tid = i ;
|
|
236 args[i].numThreads = numThreads ;
|
|
237
|
|
238 pthread_create( &threads[i], &pthreadAttr, GetAlignmentsInfo_Thread, &args[i] ) ;
|
|
239 }
|
|
240
|
|
241 for ( i = 0 ; i < numThreads ; ++i )
|
|
242 {
|
|
243 pthread_join( threads[i], NULL ) ;
|
|
244 }
|
|
245
|
|
246 pthread_attr_destroy( &pthreadAttr ) ;
|
|
247 delete[] args ;
|
|
248 delete[] threads ;
|
|
249 }
|
|
250
|
|
251 // Build the subexon graph
|
|
252 SubexonGraph subexonGraph( classifierThreshold, alignmentFiles[0], fpSubexon ) ;
|
|
253 subexonGraph.ComputeGeneIntervals() ;
|
|
254
|
|
255 // Solve gene by gene
|
|
256 int sampleCnt = alignmentFiles.size() ;
|
|
257 std::vector<Constraints> multiSampleConstraints ;
|
|
258 for ( i = 0 ; i < sampleCnt ; ++i )
|
|
259 {
|
|
260 Constraints constraints( &alignmentFiles[i] ) ;
|
|
261 constraints.SetHasMateReadIdSuffix( hasMateReadIdSuffix ) ;
|
|
262 constraints.SetUsePrimaryAsUnique( usePrimaryAsUnique ) ;
|
|
263 multiSampleConstraints.push_back( constraints ) ;
|
|
264 }
|
|
265 MultiThreadOutputTranscript outputHandler( sampleCnt, alignmentFiles[0] ) ;
|
|
266 outputHandler.SetOutputFPs( outputPrefix ) ;
|
|
267
|
|
268 if ( numThreads <= 1 )
|
|
269 {
|
|
270 TranscriptDecider transcriptDecider( FPKMFraction, classifierThreshold, txptMinReadDepth, sampleCnt, alignmentFiles[0] ) ;
|
|
271
|
|
272 transcriptDecider.SetMultiThreadOutputHandler( &outputHandler ) ;
|
|
273 transcriptDecider.SetNumThreads( numThreads ) ;
|
|
274 transcriptDecider.SetMaxDpConstraintSize( maxDpConstraintSize ) ;
|
|
275
|
|
276 int giCnt = subexonGraph.geneIntervals.size() ;
|
|
277 for ( i = 0 ; i < giCnt ; ++i )
|
|
278 {
|
|
279 struct _geneInterval gi = subexonGraph.geneIntervals[i] ;
|
|
280 struct _subexon *intervalSubexons = new struct _subexon[ gi.endIdx - gi.startIdx + 1 ] ;
|
|
281 subexonGraph.ExtractSubexons( gi.startIdx, gi.endIdx, intervalSubexons ) ;
|
|
282 printf( "%d: %d %s %d %d\n", i, gi.endIdx - gi.startIdx + 1,
|
|
283 alignmentFiles[0].GetChromName( intervalSubexons[0].chrId ),
|
|
284 gi.start + 1, gi.end + 1 ) ;
|
|
285 fflush( stdout ) ;
|
|
286
|
|
287 subexonCorrelation.ComputeCorrelation( intervalSubexons, gi.endIdx - gi.startIdx + 1, alignmentFiles[0] ) ;
|
|
288 for ( j = 0 ; j < sampleCnt ; ++j )
|
|
289 multiSampleConstraints[j].BuildConstraints( intervalSubexons, gi.endIdx - gi.startIdx + 1, gi.start, gi.end ) ;
|
|
290
|
|
291 transcriptDecider.Solve( intervalSubexons, gi.endIdx - gi.startIdx + 1, multiSampleConstraints, subexonCorrelation ) ;
|
|
292
|
|
293 for ( j = 0 ; j < gi.endIdx - gi.startIdx + 1 ; ++j )
|
|
294 {
|
|
295 delete[] intervalSubexons[j].prev ;
|
|
296 delete[] intervalSubexons[j].next ;
|
|
297 }
|
|
298 delete[] intervalSubexons ;
|
|
299 }
|
|
300 }
|
|
301 else // multi-thread case.
|
|
302 {
|
|
303 --numThreads ; // one thread is used for read in the data.
|
|
304
|
|
305 // Allocate memory
|
|
306 struct _transcriptDeciderThreadArg *pArgs = new struct _transcriptDeciderThreadArg[ numThreads ] ;
|
|
307 pthread_mutex_t ftLock ;
|
|
308 int *freeThreads ;
|
|
309 int ftCnt ;
|
|
310 pthread_cond_t fullWorkCond ;
|
|
311 pthread_attr_t pthreadAttr ;
|
|
312 pthread_t *threads ;
|
|
313 pthread_t *getConstraintsThreads ;
|
|
314 bool *initThreads ;
|
|
315
|
|
316 pthread_mutex_init( &ftLock, NULL ) ;
|
|
317 pthread_cond_init( &fullWorkCond, NULL ) ;
|
|
318 pthread_attr_init( &pthreadAttr ) ;
|
|
319 pthread_attr_setdetachstate( &pthreadAttr, PTHREAD_CREATE_JOINABLE ) ;
|
|
320
|
|
321 threads = new pthread_t[ numThreads ] ;
|
|
322 getConstraintsThreads = new pthread_t[ numThreads ] ;
|
|
323 initThreads = new bool[numThreads] ;
|
|
324 freeThreads = new int[ numThreads ] ;
|
|
325 ftCnt = numThreads ;
|
|
326 for ( i = 0 ; i < numThreads ; ++i )
|
|
327 {
|
|
328 pArgs[i].tid = i ;
|
|
329 pArgs[i].sampleCnt = sampleCnt ;
|
|
330 pArgs[i].numThreads = numThreads ;
|
|
331 pArgs[i].maxDpConstraintSize = maxDpConstraintSize ;
|
|
332 pArgs[i].FPKMFraction = FPKMFraction ;
|
|
333 pArgs[i].classifierThreshold = classifierThreshold ;
|
|
334 pArgs[i].txptMinReadDepth = txptMinReadDepth ;
|
|
335 pArgs[i].alignments = &alignmentFiles[0] ;
|
|
336 //pArgs[i].constraints = new std::vector<Constraints> ;
|
|
337 pArgs[i].outputHandler = &outputHandler ;
|
|
338
|
|
339 freeThreads[i] = i ;
|
|
340 pArgs[i].freeThreads = freeThreads ;
|
|
341 pArgs[i].ftCnt = &ftCnt ;
|
|
342 pArgs[i].ftLock = &ftLock ;
|
|
343 pArgs[i].fullWorkCond = &fullWorkCond ;
|
|
344
|
|
345 for ( j = 0 ; j < sampleCnt ; ++j )
|
|
346 {
|
|
347 Constraints constraints( &alignmentFiles[j] ) ;
|
|
348 pArgs[i].constraints.push_back( constraints ) ;
|
|
349 }
|
|
350
|
|
351 initThreads[i] = false ;
|
|
352 }
|
|
353
|
|
354
|
|
355 // Read in and distribute the work
|
|
356 int giCnt = subexonGraph.geneIntervals.size() ;
|
|
357 for ( i = 0 ; i < giCnt ; ++i )
|
|
358 {
|
|
359 struct _geneInterval gi = subexonGraph.geneIntervals[i] ;
|
|
360 struct _subexon *intervalSubexons = new struct _subexon[ gi.endIdx - gi.startIdx + 1 ] ;
|
|
361 subexonGraph.ExtractSubexons( gi.startIdx, gi.endIdx, intervalSubexons ) ;
|
|
362 subexonCorrelation.ComputeCorrelation( intervalSubexons, gi.endIdx - gi.startIdx + 1, alignmentFiles[0] ) ;
|
|
363 printf( "%d: %d %s %d %d. Free threads: %d/%d\n", i, gi.endIdx - gi.startIdx + 1,
|
|
364 alignmentFiles[0].GetChromName( intervalSubexons[0].chrId ),
|
|
365 gi.start + 1, gi.end + 1, ftCnt, numThreads + 1 ) ;
|
|
366 fflush( stdout ) ;
|
|
367
|
|
368 int gctCnt = ftCnt ;
|
|
369 if ( gctCnt > 1 && sampleCnt > 1 )
|
|
370 {
|
|
371 gctCnt = ( gctCnt < sampleCnt ? gctCnt : sampleCnt ) ;
|
|
372 struct _getConstraintsThreadArg *args = new struct _getConstraintsThreadArg[ gctCnt ] ;
|
|
373 for ( j = 0 ; j < gctCnt ; ++j )
|
|
374 {
|
|
375 args[j].pMultiSampleConstraints = &multiSampleConstraints ;
|
|
376 args[j].numThreads = gctCnt ;
|
|
377 args[j].tid = j ;
|
|
378 args[j].subexons = intervalSubexons ;
|
|
379 args[j].seCnt = gi.endIdx - gi.startIdx + 1 ;
|
|
380 args[j].start = gi.start ; args[j].end = gi.end ;
|
|
381 pthread_create( &getConstraintsThreads[j], &pthreadAttr, GetConstraints_Thread, &args[j] ) ;
|
|
382 }
|
|
383
|
|
384
|
|
385
|
|
386 for ( j = 0 ; j < gctCnt ; ++j )
|
|
387 pthread_join( getConstraintsThreads[j], NULL ) ;
|
|
388
|
|
389 delete[] args ;
|
|
390 }
|
|
391 else
|
|
392 {
|
|
393 for ( j = 0 ; j < sampleCnt ; ++j )
|
|
394 multiSampleConstraints[j].BuildConstraints( intervalSubexons, gi.endIdx - gi.startIdx + 1, gi.start, gi.end ) ;
|
|
395 }
|
|
396
|
|
397 // Search for the free queue.
|
|
398 int tag = -1 ; // get the working thread.
|
|
399 pthread_mutex_lock( &ftLock ) ;
|
|
400 if ( ftCnt == 0 )
|
|
401 {
|
|
402 pthread_cond_wait( &fullWorkCond, &ftLock ) ;
|
|
403 }
|
|
404 tag = freeThreads[ ftCnt - 1 ] ;
|
|
405 --ftCnt ;
|
|
406 pthread_mutex_unlock( &ftLock ) ;
|
|
407
|
|
408 if ( initThreads[tag] )
|
|
409 pthread_join( threads[tag], NULL ) ; // Make sure the chosen thread exits.
|
|
410
|
|
411 // Assign the subexons, the constraints and correlation content.
|
|
412 pArgs[tag].subexons = new struct _subexon[gi.endIdx - gi.startIdx + 1] ;
|
|
413 pArgs[tag].seCnt = gi.endIdx - gi.startIdx + 1 ;
|
|
414 for ( j = 0 ; j < pArgs[tag].seCnt ; ++j )
|
|
415 {
|
|
416 pArgs[tag].subexons[j] = intervalSubexons[j] ;
|
|
417 int cnt = intervalSubexons[j].prevCnt ;
|
|
418 pArgs[tag].subexons[j].prev = new int[cnt] ;
|
|
419 memcpy( pArgs[tag].subexons[j].prev, intervalSubexons[j].prev, sizeof( int ) * cnt ) ;
|
|
420 cnt = intervalSubexons[j].nextCnt ;
|
|
421 pArgs[tag].subexons[j].next = new int[cnt] ;
|
|
422 memcpy( pArgs[tag].subexons[j].next, intervalSubexons[j].next, sizeof( int ) * cnt ) ;
|
|
423 }
|
|
424
|
|
425 for ( j = 0 ; j < sampleCnt ; ++j )
|
|
426 {
|
|
427 pArgs[tag].constraints[j].Assign( multiSampleConstraints[ j ] ) ;
|
|
428 }
|
|
429 pArgs[tag].subexonCorrelation.Assign( subexonCorrelation ) ;
|
|
430 pthread_create( &threads[tag], &pthreadAttr, TranscriptDeciderSolve_Wrapper, &pArgs[tag] ) ;
|
|
431 initThreads[tag] = true ;
|
|
432 for ( j = 0 ; j < gi.endIdx - gi.startIdx + 1 ; ++j )
|
|
433 {
|
|
434 delete[] intervalSubexons[j].prev ;
|
|
435 delete[] intervalSubexons[j].next ;
|
|
436 }
|
|
437 delete[] intervalSubexons ;
|
|
438 }
|
|
439
|
|
440 for ( i = 0 ; i < numThreads ; ++i )
|
|
441 {
|
|
442 if ( initThreads[i] )
|
|
443 pthread_join( threads[i], NULL ) ;
|
|
444 }
|
|
445
|
|
446 // Release memory
|
|
447 for ( i = 0 ; i < numThreads ; ++i )
|
|
448 {
|
|
449 std::vector<Constraints>().swap( pArgs[i].constraints ) ;
|
|
450 }
|
|
451 delete []pArgs ;
|
|
452 pthread_attr_destroy( &pthreadAttr ) ;
|
|
453 pthread_mutex_destroy( &ftLock ) ;
|
|
454 pthread_cond_destroy( &fullWorkCond ) ;
|
|
455
|
|
456 delete[] threads ;
|
|
457 delete[] getConstraintsThreads ;
|
|
458 delete[] initThreads ;
|
|
459 delete[] freeThreads ;
|
|
460 } // end of else for multi-thread.
|
|
461
|
|
462 outputHandler.OutputCommandInfo( argc, argv ) ;
|
|
463 for ( i = 0 ; i < sampleCnt ; ++i )
|
|
464 {
|
|
465 char buffer[1024] ;
|
|
466 alignmentFiles[i].GetFileName( buffer ) ;
|
|
467 int separator = -1 ;
|
|
468
|
|
469 // deprive the directory.
|
|
470 for ( j = 0 ; buffer[j] ; ++j )
|
|
471 {
|
|
472 if ( buffer[j] == '/' )
|
|
473 separator = j ;
|
|
474 }
|
|
475 if ( separator != -1 )
|
|
476 {
|
|
477 ++separator ;
|
|
478 for ( j = separator ; buffer[j] ; ++j )
|
|
479 buffer[j - separator] = buffer[j] ;
|
|
480 buffer[j - separator] = '\0' ;
|
|
481 }
|
|
482 outputHandler.OutputCommentToSampleGTF( i, buffer ) ;
|
|
483 }
|
|
484 outputHandler.ComputeFPKMTPM( alignmentFiles ) ;
|
|
485 outputHandler.Flush() ;
|
|
486
|
|
487 for ( i = 0 ; i < sampleCnt ; ++i )
|
|
488 alignmentFiles[i].Close() ;
|
|
489 fclose( fpSubexon ) ;
|
|
490 return 0 ;
|
|
491 }
|