-
Notifications
You must be signed in to change notification settings - Fork 285
/
FileRecordMgr.cpp
412 lines (367 loc) · 12.5 KB
/
FileRecordMgr.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
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
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
#include "FileRecordMgr.h"
#include "ContextIntersect.h"
#include "FreeList.h"
#include "Record.h"
FileRecordMgr::FileRecordMgr(int fileIdx, ContextBase *context)
:
_bufStreamMgr(NULL),
_contextFileIdx(fileIdx),
_context(context),
_fileReader(NULL),
_fileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE),
_recordType(FileRecordTypeChecker::UNKNOWN_RECORD_TYPE),
_recordMgr(NULL),
_freeListBlockSize(512),
_useFullBamTags(false),
_headerSet(false),
_prevStart(INT_MAX),
_prevChromId(-1),
_mustBeForward(false),
_mustBeReverse(false),
_totalRecordLength(0),
_totalMergedRecordLength(0)
{
}
FileRecordMgr::~FileRecordMgr(){
if (_bufStreamMgr != NULL) {
delete _bufStreamMgr;
_bufStreamMgr = NULL;
}
if (_fileReader != NULL) {
close(); //just make sure file was closed.
delete _fileReader;
_fileReader = NULL;
}
if (_recordMgr != NULL) {
delete _recordMgr;
_recordMgr = NULL;
}
}
bool FileRecordMgr::open(){
_filename = _context->getInputFileName(_contextFileIdx);
_bufStreamMgr = new BufferedStreamMgr(_filename);
if (!_bufStreamMgr->init()) {
cerr << "Error: unable to open file or unable to determine types for file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
}
_fileType = _bufStreamMgr->getTypeChecker().getFileType();
_recordType = _bufStreamMgr->getTypeChecker().getRecordType();
if (_fileType == FileRecordTypeChecker::UNKNOWN_FILE_TYPE || _recordType == FileRecordTypeChecker::UNKNOWN_RECORD_TYPE) {
cerr << "Error: Unable to determine type for file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
}
allocateFileReader();
_recordMgr = new RecordMgr(_recordType, _freeListBlockSize);
_fileReader->setFileName(_filename.c_str());
_fileReader->setInputStream(_bufStreamMgr);
if (!_fileReader->open()) {
cerr << "Error: Types determined but can't open file " << _filename << endl;
delete _bufStreamMgr;
_bufStreamMgr = NULL;
exit(1);
}
_context->setInputFileType(_contextFileIdx, _fileType);
_context->setInputRecordType(_contextFileIdx, _recordType);
//if this is a database file, and the numFields is greater than the numFields in other DB files, update.
// TBD: This is one of many things that will need to be changed to support multiple database files in future versions.
int numFields = _bufStreamMgr->getTypeChecker().getNumFields();
if (_context->hasIntersectMethods()) {
if (_contextFileIdx == (static_cast<ContextIntersect *>(_context))->getDatabaseFileIdx() && numFields >
(static_cast<ContextIntersect *>(_context))->getMaxNumDatabaseFields()) {
(static_cast<ContextIntersect *>(_context))->setMaxNumDatabaseFields(numFields);
}
}
if (_fileType == FileRecordTypeChecker::BAM_FILE_TYPE) {
_context->setHeader(_contextFileIdx, _fileReader->getHeader());
_context->setReferences(_contextFileIdx, static_cast<BamFileReader *>(_fileReader)->getReferences());
_headerSet = true;
}
return true;
}
void FileRecordMgr::close(){
if (_bufStreamMgr != NULL) {
delete _bufStreamMgr;
_bufStreamMgr = NULL;
}
if (_fileReader != NULL) {
_fileReader->close();
delete _fileReader;
_fileReader = NULL;
}
}
bool FileRecordMgr::eof(){
return _fileReader->eof();
// return _storedRecords.empty() && _fileReader->eof() ? true: false;
}
Record *FileRecordMgr::allocateAndGetNextRecord()
{
if (!_fileReader->isOpen()) {
return NULL;
}
if (!_fileReader->readEntry()) {
return NULL;
}
if (!_headerSet && _fileReader->hasHeader()) {
_context->setHeader(_contextFileIdx, _fileReader->getHeader());
_headerSet = true;
}
Record *record = NULL;
record = _recordMgr->allocateRecord();
if (!record->initFromFile(_fileReader)) {
_recordMgr->deleteRecord(record);
return NULL;
}
// In the rare case of Bam records where both the read and it's mate failed to map,
// Ignore the record. Delete and return null
if (!(record->isUnmapped() && record->isMateUnmapped())) {
if (!record->coordsValid()) {
cerr << "Error: Invalid record in file " << _filename << ". Record is " << endl << *record << endl;
exit(1);
}
//test for sorted order, if necessary.
if (_context->getSortedInput()) {
testInputSortOrder(record);
}
}
assignChromId(record);
_totalRecordLength += (unsigned long)(record->getEndPos() - record->getStartPos());
return record;
}
void FileRecordMgr::assignChromId(Record *record) {
const QuickString &currChrom = record->getChrName();
if (currChrom != _prevChrom && _context->hasGenomeFile()) {
_prevChromId = _context->getGenomeFile()->getChromId(currChrom);
record->setChromId(_prevChromId);
} else {
record->setChromId(_prevChromId);
}
}
void FileRecordMgr::testInputSortOrder(Record *record)
{
// User specified that file must be sorted. Check that it is so.
// TBD: In future versions, we might not want/need all files to be sorted,
// even if the -sorted option is used, depending on number of input files
// and program being run. Should that occur, this block will need adjusting.
// NEK - 9/5/13
// Special: For BAM records that aren't mapped, we actually don't want
// to test the sort order. Another ugly hack sponsored by the letters B, A, and M.
if (record->isUnmapped()) {
return;
}
const QuickString &currChrom = record->getChrName();
int currStart = record->getStartPos();
if (record->isZeroLength()) {
currStart++;
}
if (currChrom != _prevChrom) {
if ( _foundChroms.find(currChrom) != _foundChroms.end()) {
//this is a different chrom than the last record had, but we've already seen this chrom.
sortError(record, false);
} else {
//new chrom has not been seen before.
//TBD: test genome file for ChromId.
if (_context->hasGenomeFile()) {
int currChromId = _context->getGenomeFile()->getChromId(currChrom);
if (currChromId < _prevChromId) {
sortError(record, true);
} else {
_prevChromId = currChromId;
}
}
_foundChroms.insert(currChrom);
_prevChrom = currChrom;
_prevStart = INT_MAX;
record->setChromId(_prevChromId);
}
} else if (currStart < _prevStart) { //same chrom as last record, but with lower startPos, so still out of order.
sortError(record, false);
}
_prevStart = currStart;
}
void FileRecordMgr::sortError(const Record *record, bool genomeFileError)
{
if (genomeFileError) {
cerr << "Error: Sorted input specified, but the file " << _filename << " has the following record with a different sort order than the genomeFile " <<
_context->getGenomeFile()->getGenomeFileName() << endl;
} else {
cerr << "Error: Sorted input specified, but the file " << _filename << " has the following out of order record" << endl;
}
cerr << *record << endl;
exit(1);
}
void FileRecordMgr::deleteRecord(const Record *record) {
_recordMgr->deleteRecord(record);
}
void FileRecordMgr::allocateFileReader()
{
switch (_fileType) {
case FileRecordTypeChecker::SINGLE_LINE_DELIM_TEXT_FILE_TYPE:
case FileRecordTypeChecker::VCF_FILE_TYPE:
_fileReader = new SingleLineDelimTextFileReader(_bufStreamMgr->getTypeChecker().getNumFields(), _bufStreamMgr->getTypeChecker().getDelimChar());
break;
case FileRecordTypeChecker::BAM_FILE_TYPE:
_fileReader = new BamFileReader();
(static_cast<BamFileReader *>(_fileReader))->setUseTags(_context->getUseFullBamTags());
(static_cast<BamFileReader *>(_fileReader))->setBamReader(_bufStreamMgr->getBamReader());
break;
default:
break;
}
}
#ifdef false
Record *FileRecordMgr::allocateAndGetNextMergedRecord(WANT_STRAND_TYPE desiredStrand, int maxDistance) {
RecordKeyList recList;
if (!allocateAndGetNextMergedRecord(recList, desiredStrand, maxDistance)) {
return NULL;
}
deleteAllMergedItemsButKey(recList);
return const_cast<Record *>(recList.getKey()); //want key to be non-const
}
bool FileRecordMgr::allocateAndGetNextMergedRecord(RecordKeyList & recList, WANT_STRAND_TYPE desiredStrand, int maxDistance)
{
if (!recList.allClear()) {
deleteMergedRecord(recList);
}
_mustBeForward = desiredStrand == SAME_STRAND_FORWARD;
_mustBeReverse = desiredStrand == SAME_STRAND_REVERSE;
Record *startRecord = tryToTakeFromStorage();
// if we couldn't use a previously stored record for starters,
//then begin with a new one that matches strand criteria.
while (startRecord == NULL) {
startRecord = allocateAndGetNextRecord();
if (startRecord == NULL) { //hit EOF!!
return false;
}
if (_mustBeForward && !startRecord->getStrand()) {
//record is reverse, wanted forward.
addToStorage(startRecord);
startRecord = NULL;
} else if (_mustBeReverse && startRecord->getStrand()) {
//record is forward, wanted reverse
addToStorage(startRecord);
startRecord = NULL;
}
}
// OK!! We have a start record!
_mustBeForward = desiredStrand == SAME_STRAND_FORWARD || (desiredStrand == SAME_STRAND_EITHER && startRecord->getStrand());
_mustBeReverse = desiredStrand == SAME_STRAND_REVERSE || (desiredStrand == SAME_STRAND_EITHER && !startRecord->getStrand());
const QuickString &currChrom = startRecord->getChrName();
_foundChroms.insert(currChrom);
bool madeComposite = false;
recList.push_back(startRecord);
recList.setKey(startRecord); //key of recList will just be the startRecord unless we're able to merge more.
bool currStrand = startRecord->getStrand();
bool mustMatchStrand = desiredStrand != ANY_STRAND;
int currEnd = startRecord->getEndPos();
//now look for more records to merge with this one.
//stop when they're out of range, not on the same chromosome, or we hit EOF.
//ignore if they don't comply with strand.
Record *nextRecord = NULL;
while (nextRecord == NULL) {
bool takenFromStorage = false;
nextRecord = mustMatchStrand ? tryToTakeFromStorage(currStrand) : tryToTakeFromStorage();
if (nextRecord == NULL) {
nextRecord = allocateAndGetNextRecord();
} else {
takenFromStorage = true;
}
if (nextRecord == NULL) { // EOF hit
break;
}
const QuickString &newChrom = nextRecord->getChrName();
if (newChrom != currChrom) { //hit a different chromosome.
if (_foundChroms.find(newChrom) == _foundChroms.end() || takenFromStorage) {
//haven't seen this chromosome before.
addToStorage(nextRecord);
break;
} else {
//different strand, but we've already seen this chrom. File is not sorted.
fprintf(stderr, "ERROR: Input file %s is not sorted by chromosome, startPos.\n", _context->getInputFileName(_contextFileIdx).c_str());
deleteRecord(nextRecord);
deleteMergedRecord(recList);
exit(1);
}
}
int nextStart = nextRecord->getStartPos();
//is the record out of range?
if (nextStart > currEnd + maxDistance) {
//yes, it's out of range.
addToStorage(nextRecord);
break;
}
//ok, they're on the same chrom and in range. Are we happy with the strand?
if (mustMatchStrand && nextRecord->getStrand() != currStrand) {
//no, we're not.
addToStorage(nextRecord);
nextRecord = NULL;
continue;
}
//everything's good! do a merge.
recList.push_back(nextRecord);
madeComposite = true;
int nextEnd = nextRecord->getEndPos();
if (nextEnd > currEnd) {
currEnd = nextEnd;
}
nextRecord = NULL;
}
if (madeComposite) {
Record *newKey = _recordMgr->allocateRecord();
(*newKey) = (*startRecord);
newKey->setEndPos(currEnd);
recList.setKey(newKey);
}
_totalMergedRecordLength += (unsigned long)(recList.getKey()->getEndPos() - recList.getKey()->getStartPos());
return true;
}
void FileRecordMgr::addToStorage(Record *record) {
_storedRecords.push(record);
}
Record *FileRecordMgr::tryToTakeFromStorage() {
Record *record = _storedRecords.empty() ? NULL : const_cast<Record *>(_storedRecords.top());
if (record != NULL) {
_storedRecords.pop();
}
return record;
}
Record *FileRecordMgr::tryToTakeFromStorage(bool strand) {
Record *record = NULL;
if(strand) {
if (_storedRecords.emptyForward()) {
return NULL;
} else {
record = const_cast<Record *>(_storedRecords.topForward());
_storedRecords.popForward();
return record;
}
} else {
if (_storedRecords.emptyReverse()) {
return NULL;
} else {
record = const_cast<Record *>(_storedRecords.topReverse());
_storedRecords.popReverse();
return record;
}
}
}
void FileRecordMgr::deleteMergedRecord(RecordKeyList &recList)
{
deleteAllMergedItemsButKey(recList);
deleteRecord(recList.getKey());
recList.setKey(NULL);
}
void FileRecordMgr::deleteAllMergedItemsButKey(RecordKeyList &recList) {
//if the key is also in the list, this method won't delete it.
for (RecordKeyList::const_iterator_type iter = recList.begin(); iter != recList.end(); iter = recList.next()) {
if (iter->value() == recList.getKey()) {
continue;
}
deleteRecord(iter->value());
}
recList.clearList();
}
#endif