ngs_server 0.1

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Files changed (284) hide show
  1. data/.gitignore +4 -0
  2. data/Gemfile +4 -0
  3. data/Rakefile +2 -0
  4. data/bin/ngs_server +58 -0
  5. data/data/holder.txt +0 -0
  6. data/ext/bamtools/CMakeLists.txt +49 -0
  7. data/ext/bamtools/LICENSE +22 -0
  8. data/ext/bamtools/README +60 -0
  9. data/ext/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf +0 -0
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  27. data/ext/bamtools/src/api/BamIndex.h +79 -0
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@@ -0,0 +1,453 @@
1
+ // Copyright 2007-2010 Baptiste Lepilleur
2
+ // Distributed under MIT license, or public domain if desired and
3
+ // recognized in your jurisdiction.
4
+ // See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
5
+
6
+ // included by json_value.cpp
7
+ // everything is within Json namespace
8
+
9
+ // //////////////////////////////////////////////////////////////////
10
+ // //////////////////////////////////////////////////////////////////
11
+ // //////////////////////////////////////////////////////////////////
12
+ // class ValueInternalArray
13
+ // //////////////////////////////////////////////////////////////////
14
+ // //////////////////////////////////////////////////////////////////
15
+ // //////////////////////////////////////////////////////////////////
16
+
17
+ ValueArrayAllocator::~ValueArrayAllocator()
18
+ {
19
+ }
20
+
21
+ // //////////////////////////////////////////////////////////////////
22
+ // class DefaultValueArrayAllocator
23
+ // //////////////////////////////////////////////////////////////////
24
+ #ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
25
+ class DefaultValueArrayAllocator : public ValueArrayAllocator
26
+ {
27
+ public: // overridden from ValueArrayAllocator
28
+ virtual ~DefaultValueArrayAllocator()
29
+ {
30
+ }
31
+
32
+ virtual ValueInternalArray *newArray()
33
+ {
34
+ return new ValueInternalArray();
35
+ }
36
+
37
+ virtual ValueInternalArray *newArrayCopy( const ValueInternalArray &other )
38
+ {
39
+ return new ValueInternalArray( other );
40
+ }
41
+
42
+ virtual void destructArray( ValueInternalArray *array )
43
+ {
44
+ delete array;
45
+ }
46
+
47
+ virtual void reallocateArrayPageIndex( Value **&indexes,
48
+ ValueInternalArray::PageIndex &indexCount,
49
+ ValueInternalArray::PageIndex minNewIndexCount )
50
+ {
51
+ ValueInternalArray::PageIndex newIndexCount = (indexCount*3)/2 + 1;
52
+ if ( minNewIndexCount > newIndexCount )
53
+ newIndexCount = minNewIndexCount;
54
+ void *newIndexes = realloc( indexes, sizeof(Value*) * newIndexCount );
55
+ if ( !newIndexes )
56
+ throw std::bad_alloc();
57
+ indexCount = newIndexCount;
58
+ indexes = static_cast<Value **>( newIndexes );
59
+ }
60
+ virtual void releaseArrayPageIndex( Value **indexes,
61
+ ValueInternalArray::PageIndex indexCount )
62
+ {
63
+ if ( indexes )
64
+ free( indexes );
65
+ }
66
+
67
+ virtual Value *allocateArrayPage()
68
+ {
69
+ return static_cast<Value *>( malloc( sizeof(Value) * ValueInternalArray::itemsPerPage ) );
70
+ }
71
+
72
+ virtual void releaseArrayPage( Value *value )
73
+ {
74
+ if ( value )
75
+ free( value );
76
+ }
77
+ };
78
+
79
+ #else // #ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
80
+ /// @todo make this thread-safe (lock when accessign batch allocator)
81
+ class DefaultValueArrayAllocator : public ValueArrayAllocator
82
+ {
83
+ public: // overridden from ValueArrayAllocator
84
+ virtual ~DefaultValueArrayAllocator()
85
+ {
86
+ }
87
+
88
+ virtual ValueInternalArray *newArray()
89
+ {
90
+ ValueInternalArray *array = arraysAllocator_.allocate();
91
+ new (array) ValueInternalArray(); // placement new
92
+ return array;
93
+ }
94
+
95
+ virtual ValueInternalArray *newArrayCopy( const ValueInternalArray &other )
96
+ {
97
+ ValueInternalArray *array = arraysAllocator_.allocate();
98
+ new (array) ValueInternalArray( other ); // placement new
99
+ return array;
100
+ }
101
+
102
+ virtual void destructArray( ValueInternalArray *array )
103
+ {
104
+ if ( array )
105
+ {
106
+ array->~ValueInternalArray();
107
+ arraysAllocator_.release( array );
108
+ }
109
+ }
110
+
111
+ virtual void reallocateArrayPageIndex( Value **&indexes,
112
+ ValueInternalArray::PageIndex &indexCount,
113
+ ValueInternalArray::PageIndex minNewIndexCount )
114
+ {
115
+ ValueInternalArray::PageIndex newIndexCount = (indexCount*3)/2 + 1;
116
+ if ( minNewIndexCount > newIndexCount )
117
+ newIndexCount = minNewIndexCount;
118
+ void *newIndexes = realloc( indexes, sizeof(Value*) * newIndexCount );
119
+ if ( !newIndexes )
120
+ throw std::bad_alloc();
121
+ indexCount = newIndexCount;
122
+ indexes = static_cast<Value **>( newIndexes );
123
+ }
124
+ virtual void releaseArrayPageIndex( Value **indexes,
125
+ ValueInternalArray::PageIndex indexCount )
126
+ {
127
+ if ( indexes )
128
+ free( indexes );
129
+ }
130
+
131
+ virtual Value *allocateArrayPage()
132
+ {
133
+ return static_cast<Value *>( pagesAllocator_.allocate() );
134
+ }
135
+
136
+ virtual void releaseArrayPage( Value *value )
137
+ {
138
+ if ( value )
139
+ pagesAllocator_.release( value );
140
+ }
141
+ private:
142
+ BatchAllocator<ValueInternalArray,1> arraysAllocator_;
143
+ BatchAllocator<Value,ValueInternalArray::itemsPerPage> pagesAllocator_;
144
+ };
145
+ #endif // #ifdef JSON_USE_SIMPLE_INTERNAL_ALLOCATOR
146
+
147
+ static ValueArrayAllocator *&arrayAllocator()
148
+ {
149
+ static DefaultValueArrayAllocator defaultAllocator;
150
+ static ValueArrayAllocator *arrayAllocator = &defaultAllocator;
151
+ return arrayAllocator;
152
+ }
153
+
154
+ static struct DummyArrayAllocatorInitializer {
155
+ DummyArrayAllocatorInitializer()
156
+ {
157
+ arrayAllocator(); // ensure arrayAllocator() statics are initialized before main().
158
+ }
159
+ } dummyArrayAllocatorInitializer;
160
+
161
+ // //////////////////////////////////////////////////////////////////
162
+ // class ValueInternalArray
163
+ // //////////////////////////////////////////////////////////////////
164
+ bool
165
+ ValueInternalArray::equals( const IteratorState &x,
166
+ const IteratorState &other )
167
+ {
168
+ return x.array_ == other.array_
169
+ && x.currentItemIndex_ == other.currentItemIndex_
170
+ && x.currentPageIndex_ == other.currentPageIndex_;
171
+ }
172
+
173
+
174
+ void
175
+ ValueInternalArray::increment( IteratorState &it )
176
+ {
177
+ JSON_ASSERT_MESSAGE( it.array_ &&
178
+ (it.currentPageIndex_ - it.array_->pages_)*itemsPerPage + it.currentItemIndex_
179
+ != it.array_->size_,
180
+ "ValueInternalArray::increment(): moving iterator beyond end" );
181
+ ++(it.currentItemIndex_);
182
+ if ( it.currentItemIndex_ == itemsPerPage )
183
+ {
184
+ it.currentItemIndex_ = 0;
185
+ ++(it.currentPageIndex_);
186
+ }
187
+ }
188
+
189
+
190
+ void
191
+ ValueInternalArray::decrement( IteratorState &it )
192
+ {
193
+ JSON_ASSERT_MESSAGE( it.array_ && it.currentPageIndex_ == it.array_->pages_
194
+ && it.currentItemIndex_ == 0,
195
+ "ValueInternalArray::decrement(): moving iterator beyond end" );
196
+ if ( it.currentItemIndex_ == 0 )
197
+ {
198
+ it.currentItemIndex_ = itemsPerPage-1;
199
+ --(it.currentPageIndex_);
200
+ }
201
+ else
202
+ {
203
+ --(it.currentItemIndex_);
204
+ }
205
+ }
206
+
207
+
208
+ Value &
209
+ ValueInternalArray::unsafeDereference( const IteratorState &it )
210
+ {
211
+ return (*(it.currentPageIndex_))[it.currentItemIndex_];
212
+ }
213
+
214
+
215
+ Value &
216
+ ValueInternalArray::dereference( const IteratorState &it )
217
+ {
218
+ JSON_ASSERT_MESSAGE( it.array_ &&
219
+ (it.currentPageIndex_ - it.array_->pages_)*itemsPerPage + it.currentItemIndex_
220
+ < it.array_->size_,
221
+ "ValueInternalArray::dereference(): dereferencing invalid iterator" );
222
+ return unsafeDereference( it );
223
+ }
224
+
225
+ void
226
+ ValueInternalArray::makeBeginIterator( IteratorState &it ) const
227
+ {
228
+ it.array_ = const_cast<ValueInternalArray *>( this );
229
+ it.currentItemIndex_ = 0;
230
+ it.currentPageIndex_ = pages_;
231
+ }
232
+
233
+
234
+ void
235
+ ValueInternalArray::makeIterator( IteratorState &it, ArrayIndex index ) const
236
+ {
237
+ it.array_ = const_cast<ValueInternalArray *>( this );
238
+ it.currentItemIndex_ = index % itemsPerPage;
239
+ it.currentPageIndex_ = pages_ + index / itemsPerPage;
240
+ }
241
+
242
+
243
+ void
244
+ ValueInternalArray::makeEndIterator( IteratorState &it ) const
245
+ {
246
+ makeIterator( it, size_ );
247
+ }
248
+
249
+
250
+ ValueInternalArray::ValueInternalArray()
251
+ : pages_( 0 )
252
+ , size_( 0 )
253
+ , pageCount_( 0 )
254
+ {
255
+ }
256
+
257
+
258
+ ValueInternalArray::ValueInternalArray( const ValueInternalArray &other )
259
+ : pages_( 0 )
260
+ , pageCount_( 0 )
261
+ , size_( other.size_ )
262
+ {
263
+ PageIndex minNewPages = other.size_ / itemsPerPage;
264
+ arrayAllocator()->reallocateArrayPageIndex( pages_, pageCount_, minNewPages );
265
+ JSON_ASSERT_MESSAGE( pageCount_ >= minNewPages,
266
+ "ValueInternalArray::reserve(): bad reallocation" );
267
+ IteratorState itOther;
268
+ other.makeBeginIterator( itOther );
269
+ Value *value;
270
+ for ( ArrayIndex index = 0; index < size_; ++index, increment(itOther) )
271
+ {
272
+ if ( index % itemsPerPage == 0 )
273
+ {
274
+ PageIndex pageIndex = index / itemsPerPage;
275
+ value = arrayAllocator()->allocateArrayPage();
276
+ pages_[pageIndex] = value;
277
+ }
278
+ new (value) Value( dereference( itOther ) );
279
+ }
280
+ }
281
+
282
+
283
+ ValueInternalArray &
284
+ ValueInternalArray::operator =( const ValueInternalArray &other )
285
+ {
286
+ ValueInternalArray temp( other );
287
+ swap( temp );
288
+ return *this;
289
+ }
290
+
291
+
292
+ ValueInternalArray::~ValueInternalArray()
293
+ {
294
+ // destroy all constructed items
295
+ IteratorState it;
296
+ IteratorState itEnd;
297
+ makeBeginIterator( it);
298
+ makeEndIterator( itEnd );
299
+ for ( ; !equals(it,itEnd); increment(it) )
300
+ {
301
+ Value *value = &dereference(it);
302
+ value->~Value();
303
+ }
304
+ // release all pages
305
+ PageIndex lastPageIndex = size_ / itemsPerPage;
306
+ for ( PageIndex pageIndex = 0; pageIndex < lastPageIndex; ++pageIndex )
307
+ arrayAllocator()->releaseArrayPage( pages_[pageIndex] );
308
+ // release pages index
309
+ arrayAllocator()->releaseArrayPageIndex( pages_, pageCount_ );
310
+ }
311
+
312
+
313
+ void
314
+ ValueInternalArray::swap( ValueInternalArray &other )
315
+ {
316
+ Value **tempPages = pages_;
317
+ pages_ = other.pages_;
318
+ other.pages_ = tempPages;
319
+ ArrayIndex tempSize = size_;
320
+ size_ = other.size_;
321
+ other.size_ = tempSize;
322
+ PageIndex tempPageCount = pageCount_;
323
+ pageCount_ = other.pageCount_;
324
+ other.pageCount_ = tempPageCount;
325
+ }
326
+
327
+ void
328
+ ValueInternalArray::clear()
329
+ {
330
+ ValueInternalArray dummy;
331
+ swap( dummy );
332
+ }
333
+
334
+
335
+ void
336
+ ValueInternalArray::resize( ArrayIndex newSize )
337
+ {
338
+ if ( newSize == 0 )
339
+ clear();
340
+ else if ( newSize < size_ )
341
+ {
342
+ IteratorState it;
343
+ IteratorState itEnd;
344
+ makeIterator( it, newSize );
345
+ makeIterator( itEnd, size_ );
346
+ for ( ; !equals(it,itEnd); increment(it) )
347
+ {
348
+ Value *value = &dereference(it);
349
+ value->~Value();
350
+ }
351
+ PageIndex pageIndex = (newSize + itemsPerPage - 1) / itemsPerPage;
352
+ PageIndex lastPageIndex = size_ / itemsPerPage;
353
+ for ( ; pageIndex < lastPageIndex; ++pageIndex )
354
+ arrayAllocator()->releaseArrayPage( pages_[pageIndex] );
355
+ size_ = newSize;
356
+ }
357
+ else if ( newSize > size_ )
358
+ resolveReference( newSize );
359
+ }
360
+
361
+
362
+ void
363
+ ValueInternalArray::makeIndexValid( ArrayIndex index )
364
+ {
365
+ // Need to enlarge page index ?
366
+ if ( index >= pageCount_ * itemsPerPage )
367
+ {
368
+ PageIndex minNewPages = (index + 1) / itemsPerPage;
369
+ arrayAllocator()->reallocateArrayPageIndex( pages_, pageCount_, minNewPages );
370
+ JSON_ASSERT_MESSAGE( pageCount_ >= minNewPages, "ValueInternalArray::reserve(): bad reallocation" );
371
+ }
372
+
373
+ // Need to allocate new pages ?
374
+ ArrayIndex nextPageIndex =
375
+ (size_ % itemsPerPage) != 0 ? size_ - (size_%itemsPerPage) + itemsPerPage
376
+ : size_;
377
+ if ( nextPageIndex <= index )
378
+ {
379
+ PageIndex pageIndex = nextPageIndex / itemsPerPage;
380
+ PageIndex pageToAllocate = (index - nextPageIndex) / itemsPerPage + 1;
381
+ for ( ; pageToAllocate-- > 0; ++pageIndex )
382
+ pages_[pageIndex] = arrayAllocator()->allocateArrayPage();
383
+ }
384
+
385
+ // Initialize all new entries
386
+ IteratorState it;
387
+ IteratorState itEnd;
388
+ makeIterator( it, size_ );
389
+ size_ = index + 1;
390
+ makeIterator( itEnd, size_ );
391
+ for ( ; !equals(it,itEnd); increment(it) )
392
+ {
393
+ Value *value = &dereference(it);
394
+ new (value) Value(); // Construct a default value using placement new
395
+ }
396
+ }
397
+
398
+ Value &
399
+ ValueInternalArray::resolveReference( ArrayIndex index )
400
+ {
401
+ if ( index >= size_ )
402
+ makeIndexValid( index );
403
+ return pages_[index/itemsPerPage][index%itemsPerPage];
404
+ }
405
+
406
+ Value *
407
+ ValueInternalArray::find( ArrayIndex index ) const
408
+ {
409
+ if ( index >= size_ )
410
+ return 0;
411
+ return &(pages_[index/itemsPerPage][index%itemsPerPage]);
412
+ }
413
+
414
+ ValueInternalArray::ArrayIndex
415
+ ValueInternalArray::size() const
416
+ {
417
+ return size_;
418
+ }
419
+
420
+ int
421
+ ValueInternalArray::distance( const IteratorState &x, const IteratorState &y )
422
+ {
423
+ return indexOf(y) - indexOf(x);
424
+ }
425
+
426
+
427
+ ValueInternalArray::ArrayIndex
428
+ ValueInternalArray::indexOf( const IteratorState &iterator )
429
+ {
430
+ if ( !iterator.array_ )
431
+ return ArrayIndex(-1);
432
+ return ArrayIndex(
433
+ (iterator.currentPageIndex_ - iterator.array_->pages_) * itemsPerPage
434
+ + iterator.currentItemIndex_ );
435
+ }
436
+
437
+
438
+ int
439
+ ValueInternalArray::compare( const ValueInternalArray &other ) const
440
+ {
441
+ int sizeDiff( size_ - other.size_ );
442
+ if ( sizeDiff != 0 )
443
+ return sizeDiff;
444
+
445
+ for ( ArrayIndex index =0; index < size_; ++index )
446
+ {
447
+ int diff = pages_[index/itemsPerPage][index%itemsPerPage].compare(
448
+ other.pages_[index/itemsPerPage][index%itemsPerPage] );
449
+ if ( diff != 0 )
450
+ return diff;
451
+ }
452
+ return 0;
453
+ }