bio-velvet_underground 0.0.1
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- checksums.yaml +7 -0
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- data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
- data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
- data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
- data/lib/bio-velvet_underground.rb +12 -0
- data/lib/bio-velvet_underground/external/VERSION +1 -0
- data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
- data/spec/binary_sequence_store_spec.rb +27 -0
- data/spec/data/1/CnyUnifiedSeq +0 -0
- data/spec/spec_helper.rb +31 -0
- metadata +456 -0
data/ext/src/src/graph.h
ADDED
@@ -0,0 +1,233 @@
|
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1
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+
/*
|
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+
Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
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3
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+
|
4
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+
This file is part of Velvet.
|
5
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+
|
6
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+
Velvet is free software; you can redistribute it and/or modify
|
7
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+
it under the terms of the GNU General Public License as published by
|
8
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+
the Free Software Foundation; either version 2 of the License, or
|
9
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+
(at your option) any later version.
|
10
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+
|
11
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+
Velvet is distributed in the hope that it will be useful,
|
12
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+
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
13
|
+
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
14
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+
GNU General Public License for more details.
|
15
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+
|
16
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+
You should have received a copy of the GNU General Public License
|
17
|
+
along with Velvet; if not, write to the Free Software
|
18
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+
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
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19
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+
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20
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+
*/
|
21
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#ifndef _GRAPH_H_
|
22
|
+
#define _GRAPH_H_
|
23
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+
|
24
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////////////////////////////////////////////////////////////
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25
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+
// Node functions
|
26
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+
////////////////////////////////////////////////////////////
|
27
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+
|
28
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//Creators/destructor
|
29
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Node *newNode(IDnum sequenceID, Coordinate start, Coordinate finish,
|
30
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+
Coordinate offset, IDnum ID, TightString * sequences,
|
31
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+
int WORDLENGTH);
|
32
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+
Node *emptyNode();
|
33
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+
void destroyNode(Node * node, Graph * graph);
|
34
|
+
|
35
|
+
// Locator
|
36
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+
IDnum getNodeID(Node * node);
|
37
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+
Node *getNodeInGraph(Graph * graph, IDnum nodeID);
|
38
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+
Node *getTwinNode(Node * node);
|
39
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+
|
40
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+
// Arc info
|
41
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+
int arcCount(Node * node);
|
42
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+
int simpleArcCount(Node * node);
|
43
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+
Arc *getArc(Node * node);
|
44
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+
boolean hasSingleArc(Node * node);
|
45
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+
|
46
|
+
// Descriptor
|
47
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+
Coordinate getNodeLength(Node * node);
|
48
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+
void appendDescriptors(Node * target, Node * source);
|
49
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+
void directlyAppendDescriptors(Node * target, Node * sourcei, Coordinate totalLength);
|
50
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+
void appendSequence(Node * node, TightString * reads,
|
51
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+
PassageMarkerI guide, Graph * graph);
|
52
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+
void splitNodeDescriptor(Node * source, Node * target, Coordinate offset);
|
53
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+
void reduceNode(Node * node);
|
54
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+
void reallocateNodeDescriptor(Node * node, Coordinate length);
|
55
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+
Nucleotide getNucleotideInNode(Node * node, Coordinate index);
|
56
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+
|
57
|
+
// Passage markers
|
58
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void insertPassageMarker(PassageMarkerI marker, Node * destination);
|
59
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PassageMarkerI getMarker(Node * node);
|
60
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void setMarker(Node * node, PassageMarkerI marker);
|
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IDnum markerCount(Node * node);
|
62
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+
|
63
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// Short read marker creation
|
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void incrementReadStartCount(Node * node, Graph * graph);
|
65
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void addReadStart(Node * node, IDnum seqID, Coordinate position,
|
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Graph * graph, Coordinate offset);
|
67
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+
void blurLastShortReadMarker(Node * node, Graph * graph);
|
68
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+
|
69
|
+
// Short read marker handling
|
70
|
+
ShortReadMarker *getNodeReads(Node * node, Graph * graph);
|
71
|
+
IDnum getNodeReadCount(Node * node, Graph * graph);
|
72
|
+
ShortReadMarker *commonNodeReads(Node * nodeA, Node * nodeB, Graph * graph,
|
73
|
+
IDnum * length);
|
74
|
+
ShortReadMarker *extractBackOfNodeReads(Node * node, Coordinate breakpoint,
|
75
|
+
Graph * graph, IDnum * length,
|
76
|
+
PassageMarkerI sourceMarker,
|
77
|
+
ShortLength * sequenceLengths);
|
78
|
+
ShortReadMarker *extractFrontOfNodeReads(Node * node,
|
79
|
+
Coordinate breakpoint,
|
80
|
+
Graph * graph, IDnum * length,
|
81
|
+
PassageMarkerI sourceMarker,
|
82
|
+
ShortLength * sequenceLengths);
|
83
|
+
|
84
|
+
// Short read marker moving around
|
85
|
+
void foldSymmetricalNodeReads(Node * node, Graph * graph);
|
86
|
+
void spreadReadIDs(ShortReadMarker * reads, IDnum readCount, Node * node,
|
87
|
+
Graph * graph);
|
88
|
+
void injectShortReads(ShortReadMarker * sourceArray, IDnum sourceLength,
|
89
|
+
Node * target, Graph * graph);
|
90
|
+
void mergeNodeReads(Node * target, Node * source, Graph * graph);
|
91
|
+
|
92
|
+
#ifndef SINGLE_COV_CAT
|
93
|
+
// Virtual coverage
|
94
|
+
void setVirtualCoverage(Node * node, Category category,
|
95
|
+
Coordinate coverage);
|
96
|
+
void incrementVirtualCoverage(Node * node, Category category,
|
97
|
+
Coordinate coverage);
|
98
|
+
Coordinate getVirtualCoverage(Node * node, Category category);
|
99
|
+
Coordinate getTotalCoverage(Node * node);
|
100
|
+
|
101
|
+
// Original virtual coverage
|
102
|
+
void setOriginalVirtualCoverage(Node * node, Category category,
|
103
|
+
Coordinate coverage);
|
104
|
+
void incrementOriginalVirtualCoverage(Node * node, Category category,
|
105
|
+
Coordinate coverage);
|
106
|
+
Coordinate getOriginalVirtualCoverage(Node * node, Category category);
|
107
|
+
|
108
|
+
#else
|
109
|
+
// Virtual coverage
|
110
|
+
void setVirtualCoverage(Node * node,
|
111
|
+
Coordinate coverage);
|
112
|
+
void incrementVirtualCoverage(Node * node,
|
113
|
+
Coordinate coverage);
|
114
|
+
Coordinate getVirtualCoverage(Node * node);
|
115
|
+
Coordinate getTotalCoverage(Node * node);
|
116
|
+
#endif
|
117
|
+
|
118
|
+
// Status
|
119
|
+
void setNodeStatus(Node * node, boolean status);
|
120
|
+
void setSingleNodeStatus(Node * node, boolean status);
|
121
|
+
boolean getNodeStatus(Node * node);
|
122
|
+
|
123
|
+
// Uniqueness
|
124
|
+
void setUniqueness(Node * node, boolean value);
|
125
|
+
boolean getUniqueness(Node * node);
|
126
|
+
|
127
|
+
// Gap markers
|
128
|
+
void appendGap(Node * node, Coordinate length, Graph * graph);
|
129
|
+
void appendNodeGaps(Node * destination, Node * source, Graph * graph);
|
130
|
+
|
131
|
+
// IO
|
132
|
+
TightString *expandNode(Node * node, int WORDLENGTH);
|
133
|
+
void appendNodeSequence(Node * node, TightString * sequence,
|
134
|
+
Coordinate writeIndex);
|
135
|
+
char *expandNodeFragment(Node * node, Coordinate contigStart,
|
136
|
+
Coordinate contigFinish, int WORDLENGTH);
|
137
|
+
|
138
|
+
////////////////////////////////////////////////////////////
|
139
|
+
// Arc functions
|
140
|
+
////////////////////////////////////////////////////////////
|
141
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+
|
142
|
+
// Creators/destructor
|
143
|
+
Arc *createArc(Node * origin, Node * destination, Graph * graph);
|
144
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+
void createAnalogousArc(Node * origin, Node * destination, Arc * refArc,
|
145
|
+
Graph * graph);
|
146
|
+
void destroyArc(Arc * arc, Graph * graph);
|
147
|
+
|
148
|
+
// Multiplicity
|
149
|
+
void setMultiplicity(Arc * arc, IDnum mult);
|
150
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+
IDnum getMultiplicity(Arc * arc);
|
151
|
+
|
152
|
+
// Extremities
|
153
|
+
Node *getOrigin(Arc * arc);
|
154
|
+
Node *getDestination(Arc * arc);
|
155
|
+
|
156
|
+
// Finding arcs
|
157
|
+
Arc *getArcBetweenNodes(Node * origin, Node * destination, Graph * graph);
|
158
|
+
Arc *getNextArc(Arc * arc);
|
159
|
+
|
160
|
+
// Lookup table option
|
161
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+
void activateArcLookupTable(Graph * graph);
|
162
|
+
void deactivateArcLookupTable(Graph * graph);
|
163
|
+
|
164
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+
////////////////////////////////////////////////////////////
|
165
|
+
// Short read marker functions
|
166
|
+
////////////////////////////////////////////////////////////
|
167
|
+
|
168
|
+
ShortReadMarker *getShortReadMarkerAtIndex(ShortReadMarker * array,
|
169
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+
IDnum index);
|
170
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+
|
171
|
+
IDnum getShortReadMarkerID(ShortReadMarker * marker);
|
172
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+
|
173
|
+
extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
|
174
|
+
extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
|
175
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+
Coordinate position);
|
176
|
+
|
177
|
+
extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
|
178
|
+
extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
|
179
|
+
ShortLength offset);
|
180
|
+
|
181
|
+
////////////////////////////////////////////////////////////
|
182
|
+
// Gap marker functions
|
183
|
+
////////////////////////////////////////////////////////////
|
184
|
+
|
185
|
+
GapMarker *getGap(Node * node, Graph * graph);
|
186
|
+
GapMarker *getNextGap(GapMarker * marker);
|
187
|
+
Coordinate getGapStart(GapMarker * marker);
|
188
|
+
Coordinate getGapFinish(GapMarker * marker);
|
189
|
+
|
190
|
+
////////////////////////////////////////////////////////////
|
191
|
+
// Graph functions
|
192
|
+
////////////////////////////////////////////////////////////
|
193
|
+
|
194
|
+
// Memory allocation
|
195
|
+
Graph *emptyGraph(IDnum sequenceCount, int wordLength);
|
196
|
+
void allocateNodeSpace(Graph * graph, IDnum nodeCount);
|
197
|
+
Node *addEmptyNodeToGraph(Graph * graph, IDnum nodeID);
|
198
|
+
void destroyGraph(Graph * graph);
|
199
|
+
|
200
|
+
// Dimensions
|
201
|
+
IDnum nodeCount(Graph * graph);
|
202
|
+
IDnum sequenceCount(Graph * graph);
|
203
|
+
void renumberNodes(Graph * graph);
|
204
|
+
int getWordLength(Graph * graph);
|
205
|
+
boolean doubleStrandedGraph(Graph * graph);
|
206
|
+
|
207
|
+
// Element status
|
208
|
+
void resetNodeStatus(Graph * graph);
|
209
|
+
|
210
|
+
// File IO
|
211
|
+
Graph *importGraph(char *filename);
|
212
|
+
void exportGraph(char *filename, Graph * graph, TightString * sequences);
|
213
|
+
Graph *readPreGraphFile(char *preGraphFilename, boolean * double_strand);
|
214
|
+
Graph *readConnectedGraphFile(char *connectedGraphFilename, boolean * double_strand);
|
215
|
+
|
216
|
+
// Read starts
|
217
|
+
void activateReadStarts(Graph * graph);
|
218
|
+
boolean readStartsAreActivated(Graph * graph);
|
219
|
+
void createNodeReadStartArrays(Graph * graph);
|
220
|
+
void orderNodeReadStartArrays(Graph * graph);
|
221
|
+
|
222
|
+
// Insert lengths
|
223
|
+
void setInsertLengths(Graph * graph, Category cat, Coordinate insertLength,
|
224
|
+
Coordinate insertLength_std_dev);
|
225
|
+
Coordinate getInsertLength(Graph * graph, Category cat);
|
226
|
+
double getInsertLength_var(Graph * graph, Category cat);
|
227
|
+
|
228
|
+
// Gaps markers
|
229
|
+
void activateGapMarkers(Graph * graph);
|
230
|
+
void deactivateGapMarkers(Graph * graph);
|
231
|
+
void sortGapMarkers(Graph * graph);
|
232
|
+
|
233
|
+
#endif
|
@@ -0,0 +1,1472 @@
|
|
1
|
+
/*
|
2
|
+
Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
|
3
|
+
|
4
|
+
This file is part of Velvet.
|
5
|
+
|
6
|
+
Velvet is free software; you can redistribute it and/or modify
|
7
|
+
it under the terms of the GNU General Public License as published by
|
8
|
+
the Free Software Foundation; either version 2 of the License, or
|
9
|
+
(at your option) any later version.
|
10
|
+
|
11
|
+
Velvet is distributed in the hope that it will be useful,
|
12
|
+
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
13
|
+
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
14
|
+
GNU General Public License for more details.
|
15
|
+
|
16
|
+
You should have received a copy of the GNU General Public License
|
17
|
+
along with Velvet; if not, write to the Free Software
|
18
|
+
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
|
19
|
+
|
20
|
+
*/
|
21
|
+
|
22
|
+
#include <stdlib.h>
|
23
|
+
#include <stdio.h>
|
24
|
+
#include <string.h>
|
25
|
+
#include <limits.h>
|
26
|
+
#include <sys/time.h>
|
27
|
+
|
28
|
+
#ifdef _OPENMP
|
29
|
+
#include <omp.h>
|
30
|
+
#endif
|
31
|
+
|
32
|
+
#include "globals.h"
|
33
|
+
#include "graph.h"
|
34
|
+
#include "passageMarker.h"
|
35
|
+
#include "readSet.h"
|
36
|
+
#include "tightString.h"
|
37
|
+
#include "recycleBin.h"
|
38
|
+
#include "utility.h"
|
39
|
+
#include "kmer.h"
|
40
|
+
#include "kmerOccurenceTable.h"
|
41
|
+
#include "roadMap.h"
|
42
|
+
|
43
|
+
#define ADENINE 0
|
44
|
+
#define CYTOSINE 1
|
45
|
+
#define GUANINE 2
|
46
|
+
#define THYMINE 3
|
47
|
+
|
48
|
+
|
49
|
+
//////////////////////////////////////////////////////////
|
50
|
+
// Node Locking
|
51
|
+
//////////////////////////////////////////////////////////
|
52
|
+
|
53
|
+
#ifdef _OPENMP
|
54
|
+
|
55
|
+
/* Array of per-node locks */
|
56
|
+
|
57
|
+
static omp_lock_t *nodeLocks = NULL;
|
58
|
+
|
59
|
+
static void
|
60
|
+
createNodeLocks(Graph *graph)
|
61
|
+
{
|
62
|
+
IDnum nbNodes;
|
63
|
+
IDnum nodeIndex;
|
64
|
+
|
65
|
+
nbNodes = nodeCount(graph) + 1;
|
66
|
+
if (nodeLocks)
|
67
|
+
free (nodeLocks);
|
68
|
+
nodeLocks = mallocOrExit(nbNodes, omp_lock_t);
|
69
|
+
|
70
|
+
#pragma omp parallel for
|
71
|
+
for (nodeIndex = 0; nodeIndex < nbNodes; nodeIndex++)
|
72
|
+
omp_init_lock(nodeLocks + nodeIndex);
|
73
|
+
}
|
74
|
+
|
75
|
+
static inline void lockNode(Node *node)
|
76
|
+
{
|
77
|
+
IDnum nodeID = getNodeID(node);
|
78
|
+
|
79
|
+
if (nodeID < 0)
|
80
|
+
nodeID = -nodeID;
|
81
|
+
omp_set_lock (nodeLocks + nodeID);
|
82
|
+
}
|
83
|
+
|
84
|
+
/* Assumes node is already locked */
|
85
|
+
static inline void lockTwoNodes(Node *node, Node *node2)
|
86
|
+
{
|
87
|
+
IDnum nodeID = getNodeID(node);
|
88
|
+
IDnum node2ID = getNodeID(node2);
|
89
|
+
|
90
|
+
if (nodeID < 0)
|
91
|
+
nodeID = -nodeID;
|
92
|
+
if (node2ID < 0)
|
93
|
+
node2ID = -node2ID;
|
94
|
+
|
95
|
+
if (nodeID == node2ID)
|
96
|
+
return;
|
97
|
+
|
98
|
+
/* Lock lowest ID first to avoid deadlocks */
|
99
|
+
if (nodeID < node2ID)
|
100
|
+
{
|
101
|
+
omp_set_lock (nodeLocks + node2ID);
|
102
|
+
}
|
103
|
+
else if (!omp_test_lock (nodeLocks + node2ID))
|
104
|
+
{
|
105
|
+
omp_unset_lock (nodeLocks + nodeID);
|
106
|
+
omp_set_lock (nodeLocks + node2ID);
|
107
|
+
omp_set_lock (nodeLocks + nodeID);
|
108
|
+
}
|
109
|
+
}
|
110
|
+
|
111
|
+
static inline void unLockTwoNodes(Node *node, Node *node2)
|
112
|
+
{
|
113
|
+
IDnum nodeID = getNodeID(node);
|
114
|
+
IDnum node2ID = getNodeID(node2);
|
115
|
+
|
116
|
+
if (nodeID < 0)
|
117
|
+
nodeID = -nodeID;
|
118
|
+
if (node2ID < 0)
|
119
|
+
node2ID = -node2ID;
|
120
|
+
|
121
|
+
omp_unset_lock (nodeLocks + nodeID);
|
122
|
+
if (nodeID != node2ID)
|
123
|
+
omp_unset_lock (nodeLocks + node2ID);
|
124
|
+
}
|
125
|
+
|
126
|
+
static inline void unLockNode(Node *node)
|
127
|
+
{
|
128
|
+
IDnum nodeID = getNodeID(node);
|
129
|
+
|
130
|
+
if (nodeID < 0)
|
131
|
+
nodeID = -nodeID;
|
132
|
+
omp_unset_lock (nodeLocks + nodeID);
|
133
|
+
}
|
134
|
+
|
135
|
+
#endif
|
136
|
+
|
137
|
+
//////////////////////////////////////////////////////////
|
138
|
+
// Node Lists
|
139
|
+
//////////////////////////////////////////////////////////
|
140
|
+
typedef struct smallNodeList_st SmallNodeList;
|
141
|
+
|
142
|
+
struct smallNodeList_st {
|
143
|
+
Node *node;
|
144
|
+
SmallNodeList *next;
|
145
|
+
} ATTRIBUTE_PACKED;
|
146
|
+
|
147
|
+
static RecycleBin *smallNodeListMemory = NULL;
|
148
|
+
|
149
|
+
#define BLOCKSIZE 1000
|
150
|
+
|
151
|
+
#ifdef _OPENMP
|
152
|
+
static void initSmallNodeListMemory(void)
|
153
|
+
{
|
154
|
+
int n = omp_get_max_threads();
|
155
|
+
|
156
|
+
#pragma omp critical
|
157
|
+
{
|
158
|
+
if (smallNodeListMemory == NULL)
|
159
|
+
smallNodeListMemory = newRecycleBinArray(n, sizeof(SmallNodeList), BLOCKSIZE);
|
160
|
+
}
|
161
|
+
}
|
162
|
+
#endif
|
163
|
+
|
164
|
+
static SmallNodeList *allocateSmallNodeList()
|
165
|
+
{
|
166
|
+
#ifdef _OPENMP
|
167
|
+
#ifdef DEBUG
|
168
|
+
if (smallNodeListMemory == NULL)
|
169
|
+
{
|
170
|
+
velvetLog("The memory for small nodes seems uninitialised, "
|
171
|
+
"this is probably a bug, aborting.\n");
|
172
|
+
abort();
|
173
|
+
}
|
174
|
+
#endif
|
175
|
+
return allocatePointer(getRecycleBinInArray(smallNodeListMemory,
|
176
|
+
omp_get_thread_num()));
|
177
|
+
#else
|
178
|
+
if (smallNodeListMemory == NULL)
|
179
|
+
smallNodeListMemory = newRecycleBin(sizeof(SmallNodeList), BLOCKSIZE);
|
180
|
+
|
181
|
+
return allocatePointer(smallNodeListMemory);
|
182
|
+
#endif
|
183
|
+
}
|
184
|
+
|
185
|
+
static void deallocateSmallNodeList(SmallNodeList * smallNodeList)
|
186
|
+
{
|
187
|
+
#ifdef _OPENMP
|
188
|
+
deallocatePointer(getRecycleBinInArray(smallNodeListMemory,
|
189
|
+
omp_get_thread_num()),
|
190
|
+
smallNodeList);
|
191
|
+
#else
|
192
|
+
deallocatePointer(smallNodeListMemory, smallNodeList);
|
193
|
+
#endif
|
194
|
+
}
|
195
|
+
|
196
|
+
static void destroySmallNodeListMemmory(void)
|
197
|
+
{
|
198
|
+
if (smallNodeListMemory != NULL)
|
199
|
+
{
|
200
|
+
#ifdef _OPENMP
|
201
|
+
destroyRecycleBinArray(smallNodeListMemory);
|
202
|
+
#else
|
203
|
+
destroyRecycleBin(smallNodeListMemory);
|
204
|
+
#endif
|
205
|
+
smallNodeListMemory = NULL;
|
206
|
+
}
|
207
|
+
}
|
208
|
+
|
209
|
+
static inline void memorizeNode(Node * node, SmallNodeList ** nodePile)
|
210
|
+
{
|
211
|
+
SmallNodeList *list = allocateSmallNodeList();
|
212
|
+
list->node = node;
|
213
|
+
list->next = *nodePile;
|
214
|
+
*nodePile = list;
|
215
|
+
#ifndef _OPENMP
|
216
|
+
setSingleNodeStatus(node, true);
|
217
|
+
#endif
|
218
|
+
}
|
219
|
+
|
220
|
+
static inline boolean isNodeMemorized(Node * node, SmallNodeList * nodePile)
|
221
|
+
{
|
222
|
+
#ifdef _OPENMP
|
223
|
+
/* SF TODO There must be a faster way to do this: bit mask, hash table, tree, ... ? */
|
224
|
+
SmallNodeList * list;
|
225
|
+
|
226
|
+
for (list = nodePile; list; list = list->next)
|
227
|
+
if (list->node == node)
|
228
|
+
return true;
|
229
|
+
|
230
|
+
return false;
|
231
|
+
#else
|
232
|
+
return getNodeStatus(node);
|
233
|
+
#endif
|
234
|
+
}
|
235
|
+
|
236
|
+
static void unMemorizeNodes(SmallNodeList ** nodePile)
|
237
|
+
{
|
238
|
+
SmallNodeList * list;
|
239
|
+
|
240
|
+
while (*nodePile) {
|
241
|
+
list = *nodePile;
|
242
|
+
*nodePile = list->next;
|
243
|
+
#ifndef _OPENMP
|
244
|
+
setSingleNodeStatus(list->node, false);
|
245
|
+
#endif
|
246
|
+
deallocateSmallNodeList(list);
|
247
|
+
}
|
248
|
+
}
|
249
|
+
|
250
|
+
///////////////////////////////////////////////////////////
|
251
|
+
// Reference Mappings
|
252
|
+
///////////////////////////////////////////////////////////
|
253
|
+
typedef struct referenceMapping_st ReferenceMapping;
|
254
|
+
|
255
|
+
struct referenceMapping_st {
|
256
|
+
IDnum referenceStart;
|
257
|
+
IDnum nodeStart;
|
258
|
+
IDnum length;
|
259
|
+
IDnum referenceID;
|
260
|
+
IDnum nodeID;
|
261
|
+
} ATTRIBUTE_PACKED;
|
262
|
+
|
263
|
+
static IDnum countMappings(char * preGraphFilename) {
|
264
|
+
FILE *file = fopen(preGraphFilename, "r");
|
265
|
+
const int maxline = MAXLINE;
|
266
|
+
char line[MAXLINE];
|
267
|
+
IDnum count = 0;
|
268
|
+
|
269
|
+
// Go past NODE blocks
|
270
|
+
while(fgets(line, maxline, file))
|
271
|
+
if (line[0] == 'S')
|
272
|
+
break;
|
273
|
+
|
274
|
+
// Count relevant lines
|
275
|
+
while(fgets(line, maxline, file))
|
276
|
+
if (line[0] != 'S')
|
277
|
+
count++;
|
278
|
+
|
279
|
+
fclose(file);
|
280
|
+
return count;
|
281
|
+
}
|
282
|
+
|
283
|
+
static ReferenceMapping * recordReferenceMappings(char * preGraphFilename, IDnum arrayLength) {
|
284
|
+
ReferenceMapping * mappings = callocOrExit(arrayLength, ReferenceMapping);
|
285
|
+
FILE *file = fopen(preGraphFilename, "r");
|
286
|
+
const int maxline = MAXLINE;
|
287
|
+
char line[MAXLINE];
|
288
|
+
ReferenceMapping * current = mappings;
|
289
|
+
IDnum referenceID;
|
290
|
+
long long_var;
|
291
|
+
long long coord1, coord2, coord3;
|
292
|
+
|
293
|
+
// Go past NODE blocks
|
294
|
+
while(fgets(line, maxline, file))
|
295
|
+
if (line[0] == 'S')
|
296
|
+
break;
|
297
|
+
|
298
|
+
sscanf(line, "SEQ\t%li\n", &long_var);
|
299
|
+
referenceID = long_var;
|
300
|
+
|
301
|
+
// Go relevant lines
|
302
|
+
while(fgets(line, maxline, file)) {
|
303
|
+
if (line[0] != 'S') {
|
304
|
+
sscanf(line, "%li\t%lli\t%lli\t%lli\n", &long_var, &coord1, &coord2, &coord3);
|
305
|
+
current->referenceID = referenceID;
|
306
|
+
current->nodeID = long_var;
|
307
|
+
current->nodeStart = coord1;
|
308
|
+
current->referenceStart = coord2;
|
309
|
+
current->length = coord3;
|
310
|
+
current++;
|
311
|
+
} else {
|
312
|
+
sscanf(line, "SEQ\t%li\n", &long_var);
|
313
|
+
referenceID = long_var;
|
314
|
+
}
|
315
|
+
}
|
316
|
+
|
317
|
+
fclose(file);
|
318
|
+
return mappings;
|
319
|
+
}
|
320
|
+
|
321
|
+
static int compareRefMaps(const void * ptrA, const void * ptrB) {
|
322
|
+
ReferenceMapping * A = (ReferenceMapping *) ptrA;
|
323
|
+
ReferenceMapping * B = (ReferenceMapping *) ptrB;
|
324
|
+
|
325
|
+
if (A->referenceID > B->referenceID)
|
326
|
+
return 1;
|
327
|
+
else if (A->referenceID < B->referenceID)
|
328
|
+
return -1;
|
329
|
+
else {
|
330
|
+
if (A->referenceStart >= B->referenceStart + B->length)
|
331
|
+
return 1;
|
332
|
+
else if (A->referenceStart + A->length <= B->referenceStart)
|
333
|
+
return -1;
|
334
|
+
else
|
335
|
+
return 0;
|
336
|
+
}
|
337
|
+
}
|
338
|
+
|
339
|
+
static ReferenceMapping * computeReferenceMappings(char * preGraphFilename, ReadSet * reads, Coordinate * referenceMappingLength, IDnum * referenceCount) {
|
340
|
+
IDnum index;
|
341
|
+
ReferenceMapping * referenceMappings;
|
342
|
+
|
343
|
+
for(index = 0; index < reads->readCount && reads->categories[index] == 2 * CATEGORIES + 2; index++)
|
344
|
+
(*referenceCount)++;
|
345
|
+
|
346
|
+
if (*referenceCount == 0) {
|
347
|
+
*referenceMappingLength = 0;
|
348
|
+
return NULL;
|
349
|
+
}
|
350
|
+
|
351
|
+
*referenceMappingLength = countMappings(preGraphFilename);
|
352
|
+
|
353
|
+
if (*referenceMappingLength == 0)
|
354
|
+
return NULL;
|
355
|
+
|
356
|
+
referenceMappings = recordReferenceMappings(preGraphFilename, *referenceMappingLength);
|
357
|
+
qsort(referenceMappings, *referenceMappingLength, sizeof(ReferenceMapping), compareRefMaps);
|
358
|
+
|
359
|
+
return referenceMappings;
|
360
|
+
}
|
361
|
+
|
362
|
+
static ReferenceMapping * findReferenceMapping(IDnum seqID, Coordinate refCoord, ReferenceMapping * referenceMappings, Coordinate referenceMappingCount) {
|
363
|
+
IDnum positive_seqID;
|
364
|
+
Coordinate leftIndex = 0;
|
365
|
+
Coordinate rightIndex = referenceMappingCount - 1;
|
366
|
+
Coordinate middleIndex;
|
367
|
+
ReferenceMapping refMap;
|
368
|
+
int comparison;
|
369
|
+
|
370
|
+
if (seqID > 0)
|
371
|
+
positive_seqID = seqID;
|
372
|
+
else
|
373
|
+
positive_seqID = -seqID;
|
374
|
+
|
375
|
+
refMap.referenceID = positive_seqID;
|
376
|
+
refMap.referenceStart = refCoord;
|
377
|
+
refMap.length = 1;
|
378
|
+
refMap.nodeStart = 0;
|
379
|
+
refMap.nodeID = 0;
|
380
|
+
|
381
|
+
if (compareRefMaps(&(referenceMappings[leftIndex]), &refMap) == 0)
|
382
|
+
return &(referenceMappings[leftIndex]);
|
383
|
+
if (compareRefMaps(&(referenceMappings[rightIndex]), &refMap) == 0)
|
384
|
+
return &(referenceMappings[rightIndex]);
|
385
|
+
|
386
|
+
while (true) {
|
387
|
+
middleIndex = (rightIndex + leftIndex) / 2;
|
388
|
+
comparison = compareRefMaps(&(referenceMappings[middleIndex]), &refMap);
|
389
|
+
|
390
|
+
if (leftIndex >= rightIndex)
|
391
|
+
return NULL;
|
392
|
+
else if (comparison == 0)
|
393
|
+
return &(referenceMappings[middleIndex]);
|
394
|
+
else if (leftIndex == middleIndex)
|
395
|
+
return NULL;
|
396
|
+
else if (comparison > 0)
|
397
|
+
rightIndex = middleIndex;
|
398
|
+
else
|
399
|
+
leftIndex = middleIndex;
|
400
|
+
}
|
401
|
+
}
|
402
|
+
|
403
|
+
///////////////////////////////////////////////////////////
|
404
|
+
// Node Mask
|
405
|
+
///////////////////////////////////////////////////////////
|
406
|
+
|
407
|
+
typedef struct nodeMask_st NodeMask;
|
408
|
+
|
409
|
+
struct nodeMask_st {
|
410
|
+
IDnum nodeID;
|
411
|
+
IDnum start;
|
412
|
+
IDnum finish;
|
413
|
+
} ATTRIBUTE_PACKED;
|
414
|
+
|
415
|
+
static int compareNodeMasks(const void * ptrA, const void * ptrB) {
|
416
|
+
NodeMask * A = (NodeMask *) ptrA;
|
417
|
+
NodeMask * B = (NodeMask *) ptrB;
|
418
|
+
|
419
|
+
if (A->nodeID < B->nodeID)
|
420
|
+
return -1;
|
421
|
+
else if (A->nodeID > B->nodeID)
|
422
|
+
return 1;
|
423
|
+
else {
|
424
|
+
if (A->start < B->start)
|
425
|
+
return -1;
|
426
|
+
else if (A->start > B->start)
|
427
|
+
return 1;
|
428
|
+
else
|
429
|
+
return 0;
|
430
|
+
}
|
431
|
+
}
|
432
|
+
|
433
|
+
static NodeMask * computeNodeMasks(ReferenceMapping * referenceMappings, Coordinate arrayLength, Graph * graph) {
|
434
|
+
NodeMask * nodeMasks;
|
435
|
+
NodeMask * currentMask;
|
436
|
+
ReferenceMapping * currentMapping = referenceMappings;
|
437
|
+
Coordinate index;
|
438
|
+
|
439
|
+
if (referenceMappings == NULL)
|
440
|
+
return NULL;
|
441
|
+
|
442
|
+
nodeMasks = callocOrExit(arrayLength, NodeMask);
|
443
|
+
currentMask = nodeMasks;
|
444
|
+
|
445
|
+
for (index = 0; index < arrayLength; index++) {
|
446
|
+
if (currentMapping->nodeID > 0) {
|
447
|
+
currentMask->nodeID = currentMapping->nodeID;
|
448
|
+
} else {
|
449
|
+
currentMask->nodeID = -currentMapping->nodeID;
|
450
|
+
}
|
451
|
+
currentMask->start = currentMapping->nodeStart;
|
452
|
+
currentMask->finish = currentMapping->nodeStart + currentMapping->length;
|
453
|
+
currentMask++;
|
454
|
+
currentMapping++;
|
455
|
+
}
|
456
|
+
|
457
|
+
qsort(nodeMasks, arrayLength, sizeof(NodeMask), compareNodeMasks);
|
458
|
+
|
459
|
+
return nodeMasks;
|
460
|
+
}
|
461
|
+
|
462
|
+
///////////////////////////////////////////////////////////
|
463
|
+
// Process
|
464
|
+
///////////////////////////////////////////////////////////
|
465
|
+
|
466
|
+
static KmerOccurenceTable *referenceGraphKmers(char *preGraphFilename,
|
467
|
+
short int accelerationBits, Graph * graph, boolean double_strand, NodeMask * nodeMasks, Coordinate nodeMaskCount)
|
468
|
+
{
|
469
|
+
FILE *file = fopen(preGraphFilename, "r");
|
470
|
+
const int maxline = MAXLINE;
|
471
|
+
char line[MAXLINE];
|
472
|
+
char c;
|
473
|
+
int wordLength;
|
474
|
+
Coordinate lineLength, kmerCount;
|
475
|
+
Kmer word;
|
476
|
+
Kmer antiWord;
|
477
|
+
KmerOccurenceTable *kmerTable;
|
478
|
+
IDnum index;
|
479
|
+
IDnum nodeID = 0;
|
480
|
+
Nucleotide nucleotide;
|
481
|
+
NodeMask * nodeMask = nodeMasks;
|
482
|
+
Coordinate nodeMaskIndex = 0;
|
483
|
+
|
484
|
+
if (file == NULL)
|
485
|
+
exitErrorf(EXIT_FAILURE, true, "Could not open %s", preGraphFilename);
|
486
|
+
|
487
|
+
// Count kmers
|
488
|
+
velvetLog("Scanning pre-graph file %s for k-mers\n",
|
489
|
+
preGraphFilename);
|
490
|
+
|
491
|
+
// First line
|
492
|
+
if (!fgets(line, maxline, file))
|
493
|
+
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
|
494
|
+
sscanf(line, "%*i\t%*i\t%i\n", &wordLength);
|
495
|
+
|
496
|
+
kmerTable = newKmerOccurenceTable(accelerationBits, wordLength);
|
497
|
+
|
498
|
+
// Read nodes
|
499
|
+
if (!fgets(line, maxline, file))
|
500
|
+
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
|
501
|
+
kmerCount = 0;
|
502
|
+
while (line[0] == 'N') {
|
503
|
+
lineLength = 0;
|
504
|
+
while ((c = getc(file)) != EOF && c != '\n')
|
505
|
+
lineLength++;
|
506
|
+
kmerCount += lineLength - wordLength + 1;
|
507
|
+
if (fgets(line, maxline, file) == NULL)
|
508
|
+
break;
|
509
|
+
}
|
510
|
+
|
511
|
+
velvetLog("%li kmers found\n", (long) kmerCount);
|
512
|
+
|
513
|
+
for(nodeMaskIndex = 0; nodeMaskIndex < nodeMaskCount; nodeMaskIndex++) {
|
514
|
+
kmerCount -= nodeMasks[nodeMaskIndex].finish -
|
515
|
+
nodeMasks[nodeMaskIndex].start;
|
516
|
+
}
|
517
|
+
|
518
|
+
nodeMaskIndex = 0;
|
519
|
+
|
520
|
+
fclose(file);
|
521
|
+
|
522
|
+
// Create table
|
523
|
+
allocateKmerOccurences(kmerCount, kmerTable);
|
524
|
+
|
525
|
+
// Fill table
|
526
|
+
file = fopen(preGraphFilename, "r");
|
527
|
+
if (file == NULL)
|
528
|
+
exitErrorf(EXIT_FAILURE, true, "Could not open %s", preGraphFilename);
|
529
|
+
|
530
|
+
if (!fgets(line, maxline, file))
|
531
|
+
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
|
532
|
+
|
533
|
+
// Read nodes
|
534
|
+
if (!fgets(line, maxline, file))
|
535
|
+
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
|
536
|
+
while (line[0] == 'N') {
|
537
|
+
nodeID++;
|
538
|
+
|
539
|
+
// Fill in the initial word :
|
540
|
+
clearKmer(&word);
|
541
|
+
clearKmer(&antiWord);
|
542
|
+
|
543
|
+
for (index = 0; index < wordLength - 1; index++) {
|
544
|
+
c = getc(file);
|
545
|
+
if (c == 'A')
|
546
|
+
nucleotide = ADENINE;
|
547
|
+
else if (c == 'C')
|
548
|
+
nucleotide = CYTOSINE;
|
549
|
+
else if (c == 'G')
|
550
|
+
nucleotide = GUANINE;
|
551
|
+
else if (c == 'T')
|
552
|
+
nucleotide = THYMINE;
|
553
|
+
else if (c == '\n')
|
554
|
+
exitErrorf(EXIT_FAILURE, true, "PreGraph file incomplete");
|
555
|
+
else
|
556
|
+
nucleotide = ADENINE;
|
557
|
+
|
558
|
+
|
559
|
+
pushNucleotide(&word, nucleotide);
|
560
|
+
if (double_strand) {
|
561
|
+
#ifdef COLOR
|
562
|
+
reversePushNucleotide(&antiWord, nucleotide);
|
563
|
+
#else
|
564
|
+
reversePushNucleotide(&antiWord, 3 - nucleotide);
|
565
|
+
#endif
|
566
|
+
}
|
567
|
+
}
|
568
|
+
|
569
|
+
// Scan through node
|
570
|
+
index = 0;
|
571
|
+
while((c = getc(file)) != '\n' && c != EOF) {
|
572
|
+
if (c == 'A')
|
573
|
+
nucleotide = ADENINE;
|
574
|
+
else if (c == 'C')
|
575
|
+
nucleotide = CYTOSINE;
|
576
|
+
else if (c == 'G')
|
577
|
+
nucleotide = GUANINE;
|
578
|
+
else if (c == 'T')
|
579
|
+
nucleotide = THYMINE;
|
580
|
+
else
|
581
|
+
nucleotide = ADENINE;
|
582
|
+
|
583
|
+
pushNucleotide(&word, nucleotide);
|
584
|
+
if (double_strand) {
|
585
|
+
#ifdef COLOR
|
586
|
+
reversePushNucleotide(&antiWord, nucleotide);
|
587
|
+
#else
|
588
|
+
reversePushNucleotide(&antiWord, 3 - nucleotide);
|
589
|
+
#endif
|
590
|
+
}
|
591
|
+
|
592
|
+
// Update mask if necessary
|
593
|
+
if (nodeMask) {
|
594
|
+
if (nodeMask->nodeID < nodeID || (nodeMask->nodeID == nodeID && index >= nodeMask->finish)) {
|
595
|
+
if (++nodeMaskIndex == nodeMaskCount)
|
596
|
+
nodeMask = NULL;
|
597
|
+
else
|
598
|
+
nodeMask++;
|
599
|
+
}
|
600
|
+
}
|
601
|
+
|
602
|
+
// Check if not masked!
|
603
|
+
if (nodeMask) {
|
604
|
+
if (nodeMask->nodeID == nodeID && index >= nodeMask->start && index < nodeMask->finish) {
|
605
|
+
index++;
|
606
|
+
continue;
|
607
|
+
}
|
608
|
+
}
|
609
|
+
|
610
|
+
if (!double_strand || compareKmers(&word, &antiWord) <= 0)
|
611
|
+
recordKmerOccurence(&word, nodeID, index, kmerTable);
|
612
|
+
else
|
613
|
+
recordKmerOccurence(&antiWord, -nodeID, getNodeLength(getNodeInGraph(graph, nodeID)) - 1 - index, kmerTable);
|
614
|
+
|
615
|
+
index++;
|
616
|
+
}
|
617
|
+
|
618
|
+
if (fgets(line, maxline, file) == NULL)
|
619
|
+
break;
|
620
|
+
}
|
621
|
+
|
622
|
+
fclose(file);
|
623
|
+
|
624
|
+
// Sort table
|
625
|
+
sortKmerOccurenceTable(kmerTable);
|
626
|
+
|
627
|
+
return kmerTable;
|
628
|
+
}
|
629
|
+
|
630
|
+
static void ghostThreadSequenceThroughGraph(TightString * tString,
|
631
|
+
KmerOccurenceTable *
|
632
|
+
kmerTable, Graph * graph,
|
633
|
+
IDnum seqID, Category category,
|
634
|
+
boolean readTracking,
|
635
|
+
boolean double_strand,
|
636
|
+
ReferenceMapping * referenceMappings,
|
637
|
+
Coordinate referenceMappingCount,
|
638
|
+
IDnum refCount,
|
639
|
+
Annotation * annotations,
|
640
|
+
IDnum annotationCount,
|
641
|
+
boolean second_in_pair)
|
642
|
+
{
|
643
|
+
Kmer word;
|
644
|
+
Kmer antiWord;
|
645
|
+
Coordinate readNucleotideIndex;
|
646
|
+
KmerOccurence *kmerOccurence;
|
647
|
+
int wordLength = getWordLength(graph);
|
648
|
+
Nucleotide nucleotide;
|
649
|
+
IDnum refID;
|
650
|
+
Coordinate refCoord;
|
651
|
+
ReferenceMapping * refMap = NULL;
|
652
|
+
Coordinate uniqueIndex = 0;
|
653
|
+
Coordinate annotIndex = 0;
|
654
|
+
IDnum annotCount = 0;
|
655
|
+
boolean reversed;
|
656
|
+
SmallNodeList * nodePile = NULL;
|
657
|
+
Annotation * annotation = annotations;
|
658
|
+
|
659
|
+
Node *node = NULL;
|
660
|
+
Node *previousNode = NULL;
|
661
|
+
|
662
|
+
// Neglect any read which will not be short paired
|
663
|
+
if ((!readTracking && category % 2 == 0)
|
664
|
+
|| category / 2 >= CATEGORIES)
|
665
|
+
return;
|
666
|
+
|
667
|
+
// Neglect any string shorter than WORDLENGTH :
|
668
|
+
if (getLength(tString) < wordLength)
|
669
|
+
return;
|
670
|
+
|
671
|
+
// Verify that all short reads are reasonnably short
|
672
|
+
if (getLength(tString) > USHRT_MAX) {
|
673
|
+
velvetLog("Short read of length %lli, longer than limit %i\n",
|
674
|
+
(long long) getLength(tString), SHRT_MAX);
|
675
|
+
velvetLog("You should better declare this sequence as long, because it genuinely is!\n");
|
676
|
+
exit(1);
|
677
|
+
}
|
678
|
+
|
679
|
+
clearKmer(&word);
|
680
|
+
clearKmer(&antiWord);
|
681
|
+
|
682
|
+
// Fill in the initial word :
|
683
|
+
for (readNucleotideIndex = 0;
|
684
|
+
readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
|
685
|
+
nucleotide = getNucleotide(readNucleotideIndex, tString);
|
686
|
+
pushNucleotide(&word, nucleotide);
|
687
|
+
if (double_strand || second_in_pair) {
|
688
|
+
#ifdef COLOR
|
689
|
+
reversePushNucleotide(&antiWord, nucleotide);
|
690
|
+
#else
|
691
|
+
reversePushNucleotide(&antiWord, 3 - nucleotide);
|
692
|
+
#endif
|
693
|
+
}
|
694
|
+
}
|
695
|
+
|
696
|
+
// Go through sequence
|
697
|
+
while (readNucleotideIndex < getLength(tString)) {
|
698
|
+
// Shift word:
|
699
|
+
nucleotide = getNucleotide(readNucleotideIndex++, tString);
|
700
|
+
pushNucleotide(&word, nucleotide);
|
701
|
+
if (double_strand || second_in_pair) {
|
702
|
+
#ifdef COLOR
|
703
|
+
reversePushNucleotide(&antiWord, nucleotide);
|
704
|
+
#else
|
705
|
+
reversePushNucleotide(&antiWord, 3 - nucleotide);
|
706
|
+
#endif
|
707
|
+
}
|
708
|
+
|
709
|
+
// Update annotation if necessary
|
710
|
+
if (annotCount < annotationCount && annotIndex == getAnnotationLength(annotation)) {
|
711
|
+
annotation = getNextAnnotation(annotation);
|
712
|
+
annotCount++;
|
713
|
+
annotIndex = 0;
|
714
|
+
}
|
715
|
+
|
716
|
+
// Search for reference mapping
|
717
|
+
if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation) && getAnnotSequenceID(annotation) <= refCount && getAnnotSequenceID(annotation) >= -refCount) {
|
718
|
+
refID = getAnnotSequenceID(annotation);
|
719
|
+
if (refID > 0)
|
720
|
+
refCoord = getStart(annotation) + annotIndex;
|
721
|
+
else
|
722
|
+
refCoord = getStart(annotation) - annotIndex;
|
723
|
+
|
724
|
+
refMap = findReferenceMapping(refID, refCoord, referenceMappings, referenceMappingCount);
|
725
|
+
// If success
|
726
|
+
if (refMap) {
|
727
|
+
if (refID > 0)
|
728
|
+
node = getNodeInGraph(graph, refMap->nodeID);
|
729
|
+
else
|
730
|
+
node = getNodeInGraph(graph, -refMap->nodeID);
|
731
|
+
} else {
|
732
|
+
node = NULL;
|
733
|
+
if (previousNode)
|
734
|
+
break;
|
735
|
+
}
|
736
|
+
}
|
737
|
+
// if not.. look in table
|
738
|
+
else {
|
739
|
+
reversed = false;
|
740
|
+
if (double_strand) {
|
741
|
+
if (compareKmers(&word, &antiWord) <= 0) {
|
742
|
+
kmerOccurence =
|
743
|
+
findKmerInKmerOccurenceTable(&word,
|
744
|
+
kmerTable);
|
745
|
+
} else {
|
746
|
+
kmerOccurence =
|
747
|
+
findKmerInKmerOccurenceTable(&antiWord,
|
748
|
+
kmerTable);
|
749
|
+
reversed = true;
|
750
|
+
}
|
751
|
+
} else {
|
752
|
+
if (!second_in_pair) {
|
753
|
+
kmerOccurence =
|
754
|
+
findKmerInKmerOccurenceTable(&word,
|
755
|
+
kmerTable);
|
756
|
+
} else {
|
757
|
+
kmerOccurence =
|
758
|
+
findKmerInKmerOccurenceTable(&antiWord,
|
759
|
+
kmerTable);
|
760
|
+
reversed = true;
|
761
|
+
}
|
762
|
+
}
|
763
|
+
|
764
|
+
if (kmerOccurence) {
|
765
|
+
if (!reversed)
|
766
|
+
node = getNodeInGraph(graph, getKmerOccurenceNodeID(kmerOccurence));
|
767
|
+
else
|
768
|
+
node = getNodeInGraph(graph, -getKmerOccurenceNodeID(kmerOccurence));
|
769
|
+
} else {
|
770
|
+
node = NULL;
|
771
|
+
if (previousNode)
|
772
|
+
break;
|
773
|
+
}
|
774
|
+
|
775
|
+
}
|
776
|
+
|
777
|
+
if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation))
|
778
|
+
annotIndex++;
|
779
|
+
else
|
780
|
+
uniqueIndex++;
|
781
|
+
|
782
|
+
previousNode = node;
|
783
|
+
|
784
|
+
// Fill in graph
|
785
|
+
if (node && !isNodeMemorized(node, nodePile))
|
786
|
+
{
|
787
|
+
#ifdef _OPENMP
|
788
|
+
lockNode(node);
|
789
|
+
#endif
|
790
|
+
incrementReadStartCount(node, graph);
|
791
|
+
#ifdef _OPENMP
|
792
|
+
unLockNode(node);
|
793
|
+
#endif
|
794
|
+
memorizeNode(node, &nodePile);
|
795
|
+
}
|
796
|
+
}
|
797
|
+
|
798
|
+
unMemorizeNodes(&nodePile);
|
799
|
+
}
|
800
|
+
|
801
|
+
static void threadSequenceThroughGraph(TightString * tString,
|
802
|
+
KmerOccurenceTable * kmerTable,
|
803
|
+
Graph * graph,
|
804
|
+
IDnum seqID, Category category,
|
805
|
+
boolean readTracking,
|
806
|
+
boolean double_strand,
|
807
|
+
ReferenceMapping * referenceMappings,
|
808
|
+
Coordinate referenceMappingCount,
|
809
|
+
IDnum refCount,
|
810
|
+
Annotation * annotations,
|
811
|
+
IDnum annotationCount,
|
812
|
+
boolean second_in_pair)
|
813
|
+
{
|
814
|
+
Kmer word;
|
815
|
+
Kmer antiWord;
|
816
|
+
Coordinate readNucleotideIndex;
|
817
|
+
Coordinate kmerIndex;
|
818
|
+
KmerOccurence *kmerOccurence;
|
819
|
+
int wordLength = getWordLength(graph);
|
820
|
+
|
821
|
+
PassageMarkerI marker = NULL_IDX;
|
822
|
+
PassageMarkerI previousMarker = NULL_IDX;
|
823
|
+
Node *node = NULL;
|
824
|
+
Node *previousNode = NULL;
|
825
|
+
Coordinate coord = 0;
|
826
|
+
Coordinate previousCoord = 0;
|
827
|
+
Nucleotide nucleotide;
|
828
|
+
boolean reversed;
|
829
|
+
|
830
|
+
IDnum refID;
|
831
|
+
Coordinate refCoord = 0;
|
832
|
+
ReferenceMapping * refMap;
|
833
|
+
Annotation * annotation = annotations;
|
834
|
+
Coordinate index = 0;
|
835
|
+
Coordinate uniqueIndex = 0;
|
836
|
+
Coordinate annotIndex = 0;
|
837
|
+
IDnum annotCount = 0;
|
838
|
+
SmallNodeList * nodePile = NULL;
|
839
|
+
|
840
|
+
// Neglect any string shorter than WORDLENGTH :
|
841
|
+
if (getLength(tString) < wordLength)
|
842
|
+
return;
|
843
|
+
|
844
|
+
clearKmer(&word);
|
845
|
+
clearKmer(&antiWord);
|
846
|
+
|
847
|
+
// Fill in the initial word :
|
848
|
+
for (readNucleotideIndex = 0;
|
849
|
+
readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
|
850
|
+
nucleotide = getNucleotide(readNucleotideIndex, tString);
|
851
|
+
pushNucleotide(&word, nucleotide);
|
852
|
+
if (double_strand || second_in_pair) {
|
853
|
+
#ifdef COLOR
|
854
|
+
reversePushNucleotide(&antiWord, nucleotide);
|
855
|
+
#else
|
856
|
+
reversePushNucleotide(&antiWord, 3 - nucleotide);
|
857
|
+
#endif
|
858
|
+
}
|
859
|
+
}
|
860
|
+
|
861
|
+
// Go through sequence
|
862
|
+
// printf("len %d\n", getLength(tString));
|
863
|
+
while (readNucleotideIndex < getLength(tString)) {
|
864
|
+
nucleotide = getNucleotide(readNucleotideIndex++, tString);
|
865
|
+
pushNucleotide(&word, nucleotide);
|
866
|
+
if (double_strand || second_in_pair) {
|
867
|
+
#ifdef COLOR
|
868
|
+
reversePushNucleotide(&antiWord, nucleotide);
|
869
|
+
#else
|
870
|
+
reversePushNucleotide(&antiWord, 3 - nucleotide);
|
871
|
+
#endif
|
872
|
+
}
|
873
|
+
|
874
|
+
// Update annotation if necessary
|
875
|
+
if (annotCount < annotationCount && annotIndex == getAnnotationLength(annotation)) {
|
876
|
+
annotation = getNextAnnotation(annotation);
|
877
|
+
annotCount++;
|
878
|
+
annotIndex = 0;
|
879
|
+
}
|
880
|
+
|
881
|
+
// Search for reference mapping
|
882
|
+
if (category == REFERENCE) {
|
883
|
+
if (referenceMappings)
|
884
|
+
refMap = findReferenceMapping(seqID, index, referenceMappings, referenceMappingCount);
|
885
|
+
else
|
886
|
+
refMap = NULL;
|
887
|
+
|
888
|
+
if (refMap) {
|
889
|
+
node = getNodeInGraph(graph, refMap->nodeID);
|
890
|
+
if (refMap->nodeID > 0) {
|
891
|
+
coord = refMap->nodeStart + (index - refMap->referenceStart);
|
892
|
+
} else {
|
893
|
+
coord = getNodeLength(node) - refMap->nodeStart - refMap->length + (index - refMap->referenceStart);
|
894
|
+
}
|
895
|
+
} else {
|
896
|
+
node = NULL;
|
897
|
+
}
|
898
|
+
}
|
899
|
+
// Search for reference-based mapping
|
900
|
+
else if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation) && getAnnotSequenceID(annotation) <= refCount && getAnnotSequenceID(annotation) >= -refCount) {
|
901
|
+
refID = getAnnotSequenceID(annotation);
|
902
|
+
if (refID > 0)
|
903
|
+
refCoord = getStart(annotation) + annotIndex;
|
904
|
+
else
|
905
|
+
refCoord = getStart(annotation) - annotIndex;
|
906
|
+
|
907
|
+
refMap = findReferenceMapping(refID, refCoord, referenceMappings, referenceMappingCount);
|
908
|
+
// If success
|
909
|
+
if (refMap) {
|
910
|
+
if (refID > 0) {
|
911
|
+
node = getNodeInGraph(graph, refMap->nodeID);
|
912
|
+
if (refMap->nodeID > 0) {
|
913
|
+
coord = refMap->nodeStart + (refCoord - refMap->referenceStart);
|
914
|
+
} else {
|
915
|
+
coord = getNodeLength(node) - refMap->nodeStart - refMap->length + (refCoord - refMap->referenceStart);
|
916
|
+
}
|
917
|
+
} else {
|
918
|
+
node = getNodeInGraph(graph, -refMap->nodeID);
|
919
|
+
if (refMap->nodeID > 0) {
|
920
|
+
coord = getNodeLength(node) - refMap->nodeStart - (refCoord - refMap->referenceStart) - 1;
|
921
|
+
} else {
|
922
|
+
coord = refMap->nodeStart + refMap->length - (refCoord - refMap->referenceStart) - 1;
|
923
|
+
}
|
924
|
+
}
|
925
|
+
} else {
|
926
|
+
node = NULL;
|
927
|
+
if (previousNode)
|
928
|
+
break;
|
929
|
+
}
|
930
|
+
}
|
931
|
+
// Search in table
|
932
|
+
else {
|
933
|
+
reversed = false;
|
934
|
+
if (double_strand) {
|
935
|
+
if (compareKmers(&word, &antiWord) <= 0) {
|
936
|
+
kmerOccurence =
|
937
|
+
findKmerInKmerOccurenceTable(&word,
|
938
|
+
kmerTable);
|
939
|
+
} else {
|
940
|
+
kmerOccurence =
|
941
|
+
findKmerInKmerOccurenceTable(&antiWord,
|
942
|
+
kmerTable);
|
943
|
+
reversed = true;
|
944
|
+
}
|
945
|
+
} else {
|
946
|
+
if (!second_in_pair) {
|
947
|
+
kmerOccurence =
|
948
|
+
findKmerInKmerOccurenceTable(&word,
|
949
|
+
kmerTable);
|
950
|
+
} else {
|
951
|
+
kmerOccurence =
|
952
|
+
findKmerInKmerOccurenceTable(&antiWord,
|
953
|
+
kmerTable);
|
954
|
+
reversed = true;
|
955
|
+
}
|
956
|
+
}
|
957
|
+
|
958
|
+
if (kmerOccurence) {
|
959
|
+
if (!reversed) {
|
960
|
+
node = getNodeInGraph(graph, getKmerOccurenceNodeID(kmerOccurence));
|
961
|
+
coord = getKmerOccurencePosition(kmerOccurence);
|
962
|
+
} else {
|
963
|
+
node = getNodeInGraph(graph, -getKmerOccurenceNodeID(kmerOccurence));
|
964
|
+
coord = getNodeLength(node) - getKmerOccurencePosition(kmerOccurence) - 1;
|
965
|
+
}
|
966
|
+
} else {
|
967
|
+
node = NULL;
|
968
|
+
if (previousNode)
|
969
|
+
break;
|
970
|
+
}
|
971
|
+
}
|
972
|
+
|
973
|
+
// Increment positions
|
974
|
+
if (annotCount < annotationCount && uniqueIndex >= getPosition(annotation))
|
975
|
+
annotIndex++;
|
976
|
+
else
|
977
|
+
uniqueIndex++;
|
978
|
+
|
979
|
+
// Fill in graph
|
980
|
+
if (node)
|
981
|
+
{
|
982
|
+
#ifdef _OPENMP
|
983
|
+
lockNode(node);
|
984
|
+
#endif
|
985
|
+
kmerIndex = readNucleotideIndex - wordLength;
|
986
|
+
|
987
|
+
if (previousNode == node
|
988
|
+
&& previousCoord == coord - 1) {
|
989
|
+
if (category / 2 >= CATEGORIES) {
|
990
|
+
setPassageMarkerFinish(marker,
|
991
|
+
kmerIndex +
|
992
|
+
1);
|
993
|
+
setFinishOffset(marker,
|
994
|
+
getNodeLength(node)
|
995
|
+
- coord - 1);
|
996
|
+
} else {
|
997
|
+
#ifndef SINGLE_COV_CAT
|
998
|
+
incrementVirtualCoverage(node, category / 2, 1);
|
999
|
+
incrementOriginalVirtualCoverage(node, category / 2, 1);
|
1000
|
+
#else
|
1001
|
+
incrementVirtualCoverage(node, 1);
|
1002
|
+
#endif
|
1003
|
+
}
|
1004
|
+
#ifdef _OPENMP
|
1005
|
+
unLockNode(node);
|
1006
|
+
#endif
|
1007
|
+
} else {
|
1008
|
+
if (category / 2 >= CATEGORIES) {
|
1009
|
+
marker =
|
1010
|
+
newPassageMarker(seqID,
|
1011
|
+
kmerIndex,
|
1012
|
+
kmerIndex + 1,
|
1013
|
+
coord,
|
1014
|
+
getNodeLength
|
1015
|
+
(node) -
|
1016
|
+
coord - 1);
|
1017
|
+
transposePassageMarker(marker,
|
1018
|
+
node);
|
1019
|
+
connectPassageMarkers
|
1020
|
+
(previousMarker, marker,
|
1021
|
+
graph);
|
1022
|
+
previousMarker = marker;
|
1023
|
+
} else {
|
1024
|
+
if (readTracking) {
|
1025
|
+
if (!isNodeMemorized(node, nodePile)) {
|
1026
|
+
addReadStart(node,
|
1027
|
+
seqID,
|
1028
|
+
coord,
|
1029
|
+
graph,
|
1030
|
+
kmerIndex);
|
1031
|
+
memorizeNode(node, &nodePile);
|
1032
|
+
} else {
|
1033
|
+
blurLastShortReadMarker
|
1034
|
+
(node, graph);
|
1035
|
+
}
|
1036
|
+
}
|
1037
|
+
|
1038
|
+
#ifndef SINGLE_COV_CAT
|
1039
|
+
incrementVirtualCoverage(node, category / 2, 1);
|
1040
|
+
incrementOriginalVirtualCoverage(node, category / 2, 1);
|
1041
|
+
#else
|
1042
|
+
incrementVirtualCoverage(node, 1);
|
1043
|
+
#endif
|
1044
|
+
}
|
1045
|
+
#ifdef _OPENMP
|
1046
|
+
lockTwoNodes(node, previousNode);
|
1047
|
+
#endif
|
1048
|
+
if (category != REFERENCE)
|
1049
|
+
createArc(previousNode, node, graph);
|
1050
|
+
#ifdef _OPENMP
|
1051
|
+
unLockTwoNodes(node, previousNode);
|
1052
|
+
#endif
|
1053
|
+
}
|
1054
|
+
|
1055
|
+
previousNode = node;
|
1056
|
+
previousCoord = coord;
|
1057
|
+
}
|
1058
|
+
index++;
|
1059
|
+
}
|
1060
|
+
// printKmer(&word);
|
1061
|
+
|
1062
|
+
if (readTracking && category / 2 < CATEGORIES)
|
1063
|
+
unMemorizeNodes(&nodePile);
|
1064
|
+
}
|
1065
|
+
|
1066
|
+
static void fillUpGraph(ReadSet * reads,
|
1067
|
+
KmerOccurenceTable * kmerTable,
|
1068
|
+
Graph * graph,
|
1069
|
+
boolean readTracking,
|
1070
|
+
boolean double_strand,
|
1071
|
+
ReferenceMapping * referenceMappings,
|
1072
|
+
Coordinate referenceMappingCount,
|
1073
|
+
IDnum refCount,
|
1074
|
+
char * roadmapFilename)
|
1075
|
+
{
|
1076
|
+
IDnum readIndex;
|
1077
|
+
RoadMapArray *roadmap = NULL;
|
1078
|
+
Coordinate *annotationOffset = NULL;
|
1079
|
+
struct timeval start, end, diff;
|
1080
|
+
|
1081
|
+
if (referenceMappings)
|
1082
|
+
{
|
1083
|
+
roadmap = importRoadMapArray(roadmapFilename);
|
1084
|
+
annotationOffset = callocOrExit(reads->readCount, Coordinate);
|
1085
|
+
for (readIndex = 1; readIndex < reads->readCount; readIndex++)
|
1086
|
+
annotationOffset[readIndex] = annotationOffset[readIndex - 1]
|
1087
|
+
+ getAnnotationCount(getRoadMapInArray(roadmap, readIndex - 1));
|
1088
|
+
}
|
1089
|
+
|
1090
|
+
resetNodeStatus(graph);
|
1091
|
+
// Allocate memory for the read pairs
|
1092
|
+
if (!readStartsAreActivated(graph))
|
1093
|
+
activateReadStarts(graph);
|
1094
|
+
|
1095
|
+
gettimeofday(&start, NULL);
|
1096
|
+
#ifdef _OPENMP
|
1097
|
+
initSmallNodeListMemory();
|
1098
|
+
createNodeLocks(graph);
|
1099
|
+
#pragma omp parallel for
|
1100
|
+
#endif
|
1101
|
+
for (readIndex = refCount; readIndex < reads->readCount; readIndex++)
|
1102
|
+
{
|
1103
|
+
Annotation * annotations = NULL;
|
1104
|
+
IDnum annotationCount = 0;
|
1105
|
+
Category category;
|
1106
|
+
boolean second_in_pair;
|
1107
|
+
|
1108
|
+
if (readIndex % 1000000 == 0)
|
1109
|
+
velvetLog("Ghost Threading through reads %ld / %ld\n",
|
1110
|
+
(long) readIndex, (long) reads->readCount);
|
1111
|
+
|
1112
|
+
category = reads->categories[readIndex];
|
1113
|
+
second_in_pair = reads->categories[readIndex] & 1 && isSecondInPair(reads, readIndex);
|
1114
|
+
|
1115
|
+
if (referenceMappings)
|
1116
|
+
{
|
1117
|
+
annotationCount = getAnnotationCount(getRoadMapInArray(roadmap, readIndex));
|
1118
|
+
annotations = getAnnotationInArray(roadmap->annotations, annotationOffset[readIndex]);
|
1119
|
+
}
|
1120
|
+
|
1121
|
+
ghostThreadSequenceThroughGraph(getTightStringInArray(reads->tSequences, readIndex),
|
1122
|
+
kmerTable,
|
1123
|
+
graph, readIndex + 1,
|
1124
|
+
category,
|
1125
|
+
readTracking, double_strand,
|
1126
|
+
referenceMappings, referenceMappingCount,
|
1127
|
+
refCount, annotations, annotationCount,
|
1128
|
+
second_in_pair);
|
1129
|
+
}
|
1130
|
+
createNodeReadStartArrays(graph);
|
1131
|
+
gettimeofday(&end, NULL);
|
1132
|
+
timersub(&end, &start, &diff);
|
1133
|
+
velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", (long) diff.tv_sec, (long) diff.tv_usec);
|
1134
|
+
|
1135
|
+
gettimeofday(&start, NULL);
|
1136
|
+
#ifdef _OPENMP
|
1137
|
+
int threads = omp_get_max_threads();
|
1138
|
+
if (threads > 32)
|
1139
|
+
threads = 32;
|
1140
|
+
|
1141
|
+
#pragma omp parallel for num_threads(threads)
|
1142
|
+
#endif
|
1143
|
+
for (readIndex = 0; readIndex < reads->readCount; readIndex++)
|
1144
|
+
{
|
1145
|
+
Annotation * annotations = NULL;
|
1146
|
+
IDnum annotationCount = 0;
|
1147
|
+
Category category;
|
1148
|
+
boolean second_in_pair;
|
1149
|
+
|
1150
|
+
if (readIndex % 1000000 == 0)
|
1151
|
+
velvetLog("Threading through reads %li / %li\n",
|
1152
|
+
(long) readIndex, (long) reads->readCount);
|
1153
|
+
|
1154
|
+
category = reads->categories[readIndex];
|
1155
|
+
second_in_pair = reads->categories[readIndex] % 2 && isSecondInPair(reads, readIndex);
|
1156
|
+
|
1157
|
+
if (referenceMappings)
|
1158
|
+
{
|
1159
|
+
annotationCount = getAnnotationCount(getRoadMapInArray(roadmap, readIndex));
|
1160
|
+
annotations = getAnnotationInArray(roadmap->annotations, annotationOffset[readIndex]);
|
1161
|
+
}
|
1162
|
+
|
1163
|
+
threadSequenceThroughGraph(getTightStringInArray(reads->tSequences, readIndex),
|
1164
|
+
kmerTable,
|
1165
|
+
graph, readIndex + 1, category,
|
1166
|
+
readTracking, double_strand,
|
1167
|
+
referenceMappings, referenceMappingCount,
|
1168
|
+
refCount, annotations, annotationCount, second_in_pair);
|
1169
|
+
}
|
1170
|
+
gettimeofday(&end, NULL);
|
1171
|
+
timersub(&end, &start, &diff);
|
1172
|
+
velvetLog(" === Threaded in %ld.%06ld s\n", (long) diff.tv_sec, (long) diff.tv_usec);
|
1173
|
+
|
1174
|
+
#ifdef _OPENMP
|
1175
|
+
free(nodeLocks);
|
1176
|
+
nodeLocks = NULL;
|
1177
|
+
#endif
|
1178
|
+
|
1179
|
+
if (referenceMappings)
|
1180
|
+
{
|
1181
|
+
destroyRoadMapArray(roadmap);
|
1182
|
+
free (annotationOffset);
|
1183
|
+
}
|
1184
|
+
|
1185
|
+
orderNodeReadStartArrays(graph);
|
1186
|
+
|
1187
|
+
destroySmallNodeListMemmory();
|
1188
|
+
|
1189
|
+
destroyKmerOccurenceTable(kmerTable);
|
1190
|
+
}
|
1191
|
+
|
1192
|
+
Graph *importPreGraph(char *preGraphFilename, ReadSet * reads, char * roadmapFilename,
|
1193
|
+
boolean readTracking, short int accelerationBits)
|
1194
|
+
{
|
1195
|
+
boolean double_strand = false;
|
1196
|
+
Graph *graph = readPreGraphFile(preGraphFilename, &double_strand);
|
1197
|
+
Coordinate referenceMappingCount = 0;
|
1198
|
+
IDnum referenceCount = 0;
|
1199
|
+
|
1200
|
+
if (nodeCount(graph) == 0)
|
1201
|
+
return graph;
|
1202
|
+
|
1203
|
+
// If necessary compile reference -> node
|
1204
|
+
ReferenceMapping * referenceMappings = computeReferenceMappings(preGraphFilename, reads, &referenceMappingCount, &referenceCount);
|
1205
|
+
// Node -> reference maps
|
1206
|
+
NodeMask * nodeMasks = computeNodeMasks(referenceMappings, referenceMappingCount, graph);
|
1207
|
+
|
1208
|
+
// Map k-mers to nodes
|
1209
|
+
KmerOccurenceTable *kmerTable =
|
1210
|
+
referenceGraphKmers(preGraphFilename, accelerationBits, graph, double_strand, nodeMasks, referenceMappingCount);
|
1211
|
+
|
1212
|
+
free(nodeMasks);
|
1213
|
+
|
1214
|
+
// Map sequences -> kmers -> nodes
|
1215
|
+
fillUpGraph(reads, kmerTable, graph, readTracking, double_strand, referenceMappings, referenceMappingCount, referenceCount, roadmapFilename);
|
1216
|
+
|
1217
|
+
free(referenceMappings);
|
1218
|
+
|
1219
|
+
return graph;
|
1220
|
+
}
|
1221
|
+
|
1222
|
+
static void addReadsToGraph(TightString * tString,
|
1223
|
+
KmerOccurenceTable * kmerTable,
|
1224
|
+
Graph * graph,
|
1225
|
+
IDnum seqID, Category category,
|
1226
|
+
boolean readTracking,
|
1227
|
+
boolean double_strand,
|
1228
|
+
boolean second_in_pair)
|
1229
|
+
{
|
1230
|
+
Kmer word;
|
1231
|
+
Kmer antiWord;
|
1232
|
+
Coordinate readNucleotideIndex;
|
1233
|
+
Coordinate kmerIndex;
|
1234
|
+
KmerOccurence *kmerOccurence;
|
1235
|
+
int wordLength = getWordLength(graph);
|
1236
|
+
|
1237
|
+
Node *node = NULL;
|
1238
|
+
Node *previousNode = NULL;
|
1239
|
+
Coordinate coord = 0;
|
1240
|
+
Coordinate previousCoord = 0;
|
1241
|
+
Nucleotide nucleotide;
|
1242
|
+
boolean reversed;
|
1243
|
+
|
1244
|
+
Coordinate index = 0;
|
1245
|
+
SmallNodeList * nodePile = NULL;
|
1246
|
+
|
1247
|
+
// Neglect any read which will not be short paired
|
1248
|
+
if (category / 2 >= CATEGORIES)
|
1249
|
+
return;
|
1250
|
+
|
1251
|
+
// Neglect any string shorter than WORDLENGTH :
|
1252
|
+
if (getLength(tString) < wordLength)
|
1253
|
+
return;
|
1254
|
+
|
1255
|
+
clearKmer(&word);
|
1256
|
+
clearKmer(&antiWord);
|
1257
|
+
|
1258
|
+
// Fill in the initial word :
|
1259
|
+
for (readNucleotideIndex = 0;
|
1260
|
+
readNucleotideIndex < wordLength - 1; readNucleotideIndex++) {
|
1261
|
+
nucleotide = getNucleotide(readNucleotideIndex, tString);
|
1262
|
+
pushNucleotide(&word, nucleotide);
|
1263
|
+
if (double_strand || second_in_pair) {
|
1264
|
+
#ifdef COLOR
|
1265
|
+
reversePushNucleotide(&antiWord, nucleotide);
|
1266
|
+
#else
|
1267
|
+
reversePushNucleotide(&antiWord, 3 - nucleotide);
|
1268
|
+
#endif
|
1269
|
+
}
|
1270
|
+
}
|
1271
|
+
|
1272
|
+
// Go through sequence
|
1273
|
+
// printf("len %d\n", getLength(tString));
|
1274
|
+
while (readNucleotideIndex < getLength(tString)) {
|
1275
|
+
nucleotide = getNucleotide(readNucleotideIndex++, tString);
|
1276
|
+
pushNucleotide(&word, nucleotide);
|
1277
|
+
if (double_strand || second_in_pair) {
|
1278
|
+
#ifdef COLOR
|
1279
|
+
reversePushNucleotide(&antiWord, nucleotide);
|
1280
|
+
#else
|
1281
|
+
reversePushNucleotide(&antiWord, 3 - nucleotide);
|
1282
|
+
#endif
|
1283
|
+
}
|
1284
|
+
|
1285
|
+
// Search in table
|
1286
|
+
reversed = false;
|
1287
|
+
if (double_strand) {
|
1288
|
+
if (compareKmers(&word, &antiWord) <= 0) {
|
1289
|
+
kmerOccurence =
|
1290
|
+
findKmerInKmerOccurenceTable(&word,
|
1291
|
+
kmerTable);
|
1292
|
+
} else {
|
1293
|
+
kmerOccurence =
|
1294
|
+
findKmerInKmerOccurenceTable(&antiWord,
|
1295
|
+
kmerTable);
|
1296
|
+
reversed = true;
|
1297
|
+
}
|
1298
|
+
} else {
|
1299
|
+
if (!second_in_pair) {
|
1300
|
+
kmerOccurence =
|
1301
|
+
findKmerInKmerOccurenceTable(&word,
|
1302
|
+
kmerTable);
|
1303
|
+
} else {
|
1304
|
+
kmerOccurence =
|
1305
|
+
findKmerInKmerOccurenceTable(&antiWord,
|
1306
|
+
kmerTable);
|
1307
|
+
reversed = true;
|
1308
|
+
}
|
1309
|
+
}
|
1310
|
+
|
1311
|
+
if (kmerOccurence) {
|
1312
|
+
if (!reversed) {
|
1313
|
+
node = getNodeInGraph(graph, getKmerOccurenceNodeID(kmerOccurence));
|
1314
|
+
coord = getKmerOccurencePosition(kmerOccurence);
|
1315
|
+
} else {
|
1316
|
+
node = getNodeInGraph(graph, -getKmerOccurenceNodeID(kmerOccurence));
|
1317
|
+
coord = getNodeLength(node) - getKmerOccurencePosition(kmerOccurence) - 1;
|
1318
|
+
}
|
1319
|
+
} else {
|
1320
|
+
node = NULL;
|
1321
|
+
if (previousNode)
|
1322
|
+
break;
|
1323
|
+
}
|
1324
|
+
|
1325
|
+
// Fill in graph
|
1326
|
+
if (node)
|
1327
|
+
{
|
1328
|
+
#ifdef _OPENMP
|
1329
|
+
lockNode(node);
|
1330
|
+
#endif
|
1331
|
+
kmerIndex = readNucleotideIndex - wordLength;
|
1332
|
+
|
1333
|
+
if (previousNode != node || previousCoord != coord -1) {
|
1334
|
+
if (!isNodeMemorized(node, nodePile)) {
|
1335
|
+
addReadStart(node,
|
1336
|
+
seqID,
|
1337
|
+
coord,
|
1338
|
+
graph,
|
1339
|
+
kmerIndex);
|
1340
|
+
memorizeNode(node, &nodePile);
|
1341
|
+
} else {
|
1342
|
+
blurLastShortReadMarker
|
1343
|
+
(node, graph);
|
1344
|
+
}
|
1345
|
+
}
|
1346
|
+
#ifdef _OPENMP
|
1347
|
+
unLockNode(node);
|
1348
|
+
#endif
|
1349
|
+
previousNode = node;
|
1350
|
+
previousCoord = coord;
|
1351
|
+
}
|
1352
|
+
index++;
|
1353
|
+
}
|
1354
|
+
// printKmer(&word);
|
1355
|
+
|
1356
|
+
if (category / 2 < CATEGORIES)
|
1357
|
+
unMemorizeNodes(&nodePile);
|
1358
|
+
}
|
1359
|
+
|
1360
|
+
static void fillUpConnectedGraph(ReadSet * reads,
|
1361
|
+
KmerOccurenceTable * kmerTable,
|
1362
|
+
Graph * graph,
|
1363
|
+
boolean readTracking,
|
1364
|
+
boolean double_strand)
|
1365
|
+
{
|
1366
|
+
IDnum refCount = 0; // refs not present in connected graphs
|
1367
|
+
IDnum readIndex;
|
1368
|
+
struct timeval start, end, diff;
|
1369
|
+
|
1370
|
+
resetNodeStatus(graph);
|
1371
|
+
// Allocate memory for the read pairs
|
1372
|
+
if (!readStartsAreActivated(graph))
|
1373
|
+
activateReadStarts(graph);
|
1374
|
+
|
1375
|
+
gettimeofday(&start, NULL);
|
1376
|
+
#ifdef _OPENMP
|
1377
|
+
initSmallNodeListMemory();
|
1378
|
+
createNodeLocks(graph);
|
1379
|
+
#pragma omp parallel for
|
1380
|
+
#endif
|
1381
|
+
for (readIndex = refCount; readIndex < reads->readCount; readIndex++)
|
1382
|
+
{
|
1383
|
+
Category category;
|
1384
|
+
boolean second_in_pair;
|
1385
|
+
|
1386
|
+
if (readIndex % 1000000 == 0)
|
1387
|
+
velvetLog("Ghost Threading through reads %ld / %ld\n",
|
1388
|
+
(long) readIndex, (long) reads->readCount);
|
1389
|
+
|
1390
|
+
category = reads->categories[readIndex];
|
1391
|
+
second_in_pair = reads->categories[readIndex] & 1 && isSecondInPair(reads, readIndex);
|
1392
|
+
|
1393
|
+
// referenceMappings = NULL, referenceMappingCount = 0
|
1394
|
+
// refCount = 0, annotations = NULL, annotationCount = 0
|
1395
|
+
ghostThreadSequenceThroughGraph(getTightStringInArray(reads->tSequences, readIndex),
|
1396
|
+
kmerTable,
|
1397
|
+
graph, readIndex + 1,
|
1398
|
+
category,
|
1399
|
+
readTracking, double_strand,
|
1400
|
+
NULL, 0,
|
1401
|
+
0, NULL, 0,
|
1402
|
+
second_in_pair);
|
1403
|
+
}
|
1404
|
+
createNodeReadStartArrays(graph);
|
1405
|
+
gettimeofday(&end, NULL);
|
1406
|
+
timersub(&end, &start, &diff);
|
1407
|
+
velvetLog(" === Ghost-Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec);
|
1408
|
+
|
1409
|
+
gettimeofday(&start, NULL);
|
1410
|
+
#ifdef _OPENMP
|
1411
|
+
int threads = omp_get_max_threads();
|
1412
|
+
if (threads > 32)
|
1413
|
+
threads = 32;
|
1414
|
+
|
1415
|
+
#pragma omp parallel for num_threads(threads)
|
1416
|
+
#endif
|
1417
|
+
for (readIndex = 0; readIndex < reads->readCount; readIndex++)
|
1418
|
+
{
|
1419
|
+
Category category;
|
1420
|
+
boolean second_in_pair;
|
1421
|
+
|
1422
|
+
if (readIndex % 1000000 == 0)
|
1423
|
+
velvetLog("Adding reads %li / %li\n",
|
1424
|
+
(long) readIndex, (long) reads->readCount);
|
1425
|
+
|
1426
|
+
category = reads->categories[readIndex];
|
1427
|
+
second_in_pair = reads->categories[readIndex] % 2 && isSecondInPair(reads, readIndex);
|
1428
|
+
|
1429
|
+
addReadsToGraph(getTightStringInArray(reads->tSequences, readIndex),
|
1430
|
+
kmerTable,
|
1431
|
+
graph, readIndex + 1, category,
|
1432
|
+
readTracking, double_strand, second_in_pair);
|
1433
|
+
}
|
1434
|
+
gettimeofday(&end, NULL);
|
1435
|
+
timersub(&end, &start, &diff);
|
1436
|
+
velvetLog(" === Threaded in %ld.%06ld s\n", diff.tv_sec, diff.tv_usec);
|
1437
|
+
|
1438
|
+
#ifdef _OPENMP
|
1439
|
+
free(nodeLocks);
|
1440
|
+
nodeLocks = NULL;
|
1441
|
+
#endif
|
1442
|
+
|
1443
|
+
orderNodeReadStartArrays(graph);
|
1444
|
+
|
1445
|
+
destroySmallNodeListMemmory();
|
1446
|
+
|
1447
|
+
destroyKmerOccurenceTable(kmerTable);
|
1448
|
+
}
|
1449
|
+
|
1450
|
+
Graph *importConnectedGraph(char *connectedGraphFilename, ReadSet * reads, char * roadmapFilename,
|
1451
|
+
boolean readTracking, short int accelerationBits)
|
1452
|
+
{
|
1453
|
+
boolean double_strand = false;
|
1454
|
+
Graph *graph = readConnectedGraphFile(connectedGraphFilename, &double_strand);
|
1455
|
+
|
1456
|
+
if (nodeCount(graph) == 0)
|
1457
|
+
return graph;
|
1458
|
+
|
1459
|
+
if (readTracking) {
|
1460
|
+
Coordinate referenceMappingCount = 0;
|
1461
|
+
NodeMask * nodeMasks = NULL;
|
1462
|
+
|
1463
|
+
// Map k-mers to nodes
|
1464
|
+
KmerOccurenceTable *kmerTable =
|
1465
|
+
referenceGraphKmers(connectedGraphFilename, accelerationBits, graph, doubleStrandedGraph(graph), nodeMasks, referenceMappingCount);
|
1466
|
+
|
1467
|
+
// Map sequences -> kmers -> nodes
|
1468
|
+
fillUpConnectedGraph(reads, kmerTable, graph, readTracking, double_strand);
|
1469
|
+
}
|
1470
|
+
|
1471
|
+
return graph;
|
1472
|
+
}
|