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jazz/11-05-04: velvetg.log

File velvetg.log, 114.8 KB (added by jazz, 13 years ago)

Line
1	Flat profile:
2
3	Each sample counts as 0.01 seconds.
4	% cumulative self self total
5	time seconds seconds calls ms/call ms/call name
6	83.33 0.45 0.45 1 450.00 450.00 sortKmerOccurenceTable
7	5.56 0.48 0.03 998100 0.00 0.00 compareKmers
8	3.70 0.50 0.02 318428 0.00 0.00 findKmerInKmerOccurenceTable
9	1.85 0.51 0.01 153040 0.00 0.00 incrementVirtualCoverage
10	1.85 0.52 0.01 69675 0.00 0.00 copyKmers
11	1.85 0.53 0.01 3193 0.00 0.00 addPreNodeToPreGraph_pg
12	1.85 0.54 0.01 1 10.00 10.00 createNodeReadStartArrays
13	0.00 0.54 0.00 638766 0.00 0.00 pushNucleotide
14	0.00 0.54 0.00 453662 0.00 0.00 reversePushNucleotide
15	0.00 0.54 0.00 421263 0.00 0.00 velvetFprintf
16	0.00 0.54 0.00 397647 0.00 0.00 getLength
17	0.00 0.54 0.00 384910 0.00 0.00 getKmerKey
18	0.00 0.54 0.00 382428 0.00 0.00 getNucleotide
19	0.00 0.54 0.00 352440 0.00 0.00 getNodeInGraph
20	0.00 0.54 0.00 306080 0.00 0.00 getKmerOccurenceNodeID
21	0.00 0.54 0.00 156159 0.00 0.00 getNodeStatus
22	0.00 0.54 0.00 153040 0.00 0.00 getKmerOccurencePosition
23	0.00 0.54 0.00 153040 0.00 0.00 incrementOriginalVirtualCoverage
24	0.00 0.54 0.00 118903 0.00 0.00 getNodeLength
25	0.00 0.54 0.00 89052 0.00 0.00 getAnnotationLength
26	0.00 0.54 0.00 70399 0.00 0.00 getNucleotideChar
27	0.00 0.54 0.00 70399 0.00 0.00 writeNucleotideAtPosition
28	0.00 0.54 0.00 66482 0.00 0.00 recordKmerOccurence
29	0.00 0.54 0.00 51088 0.00 0.00 popNucleotide
30	0.00 0.54 0.00 20844 0.00 0.00 getFinish
31	0.00 0.54 0.00 20582 0.00 0.00 getStart
32	0.00 0.54 0.00 17234 0.00 0.00 nodeCount
33	0.00 0.54 0.00 15744 0.00 0.00 getPreNodeLength_pg
34	0.00 0.54 0.00 14519 0.00 0.00 getShortReadMarkerID
35	0.00 0.54 0.00 13741 0.00 0.00 getAnnotSequenceID
36	0.00 0.54 0.00 13539 0.00 0.00 getPosition
37	0.00 0.54 0.00 13140 0.00 0.00 getPreArc_pg
38	0.00 0.54 0.00 12767 0.00 0.00 getDestination_pg
39	0.00 0.54 0.00 12310 0.00 0.00 getNextAnnotation
40	0.00 0.54 0.00 11194 0.00 0.00 sequenceCount_pg
41	0.00 0.54 0.00 10691 0.00 0.00 getShortReadMarkerAtIndex
42	0.00 0.54 0.00 10675 0.00 0.00 getInsertionMarkerPosition
43	0.00 0.54 0.00 10594 0.00 0.00 clearKmer
44	0.00 0.54 0.00 10000 0.00 0.00 getAnnotationCount
45	0.00 0.54 0.00 10000 0.00 0.00 getRoadMapInArray
46	0.00 0.54 0.00 9792 0.00 0.00 setSingleNodeStatus
47	0.00 0.54 0.00 9287 0.00 0.00 preNodeCount_pg
48	0.00 0.54 0.00 8313 0.00 0.00 hasSinglePreArc_pg
49	0.00 0.54 0.00 8272 0.00 0.00 getNodeID
50	0.00 0.54 0.00 8000 0.00 0.00 getTightStringInArray
51	0.00 0.54 0.00 7713 0.00 0.00 simpleArcCount
52	0.00 0.54 0.00 7103 0.00 0.00 getTwinNode
53	0.00 0.54 0.00 6563 0.00 0.00 getFinishID
54	0.00 0.54 0.00 6089 0.00 0.00 createPreArc_pg
55	0.00 0.54 0.00 6010 0.00 0.00 sequenceCount
56	0.00 0.54 0.00 5940 0.00 0.00 allocatePointer
57	0.00 0.54 0.00 5869 0.00 0.00 deallocatePointer
58	0.00 0.54 0.00 5789 0.00 0.00 getNextPreArc_pg
59	0.00 0.54 0.00 5789 0.00 0.00 removePreArcFromList_pg
60	0.00 0.54 0.00 5645 0.00 0.00 getArc
61	0.00 0.54 0.00 5441 0.00 0.00 getStartID
62	0.00 0.54 0.00 4924 0.00 0.00 setStartID
63	0.00 0.54 0.00 4665 0.00 0.00 callocOrExit3
64	0.00 0.54 0.00 4295 0.00 0.00 getWordLength
65	0.00 0.54 0.00 4137 0.00 0.00 getMarker
66	0.00 0.54 0.00 4088 0.00 0.00 getPreNodeInPreGraph_pg
67	0.00 0.54 0.00 3845 0.00 0.00 getShortReadMarkerOffset
68	0.00 0.54 0.00 3845 0.00 0.00 getShortReadMarkerPosition
69	0.00 0.54 0.00 3681 0.00 0.00 setFinishID
70	0.00 0.54 0.00 3341 0.00 0.00 getOtherEnd_pg
71	0.00 0.54 0.00 3341 0.00 0.00 isLoop_pg
72	0.00 0.54 0.00 3338 0.00 0.00 appendDescriptors_pg
73	0.00 0.54 0.00 3239 0.00 0.00 getNodeReadCount
74	0.00 0.54 0.00 3239 0.00 0.00 getNodeReads
75	0.00 0.54 0.00 3173 0.00 0.00 mallocOrExit3
76	0.00 0.54 0.00 2966 0.00 0.00 getUniqueness
77	0.00 0.54 0.00 2896 0.00 0.00 allocArrayAllocate
78	0.00 0.54 0.00 2896 0.00 0.00 destroyPreNode_pg
79	0.00 0.54 0.00 2895 0.00 0.00 allocArrayFree
80	0.00 0.54 0.00 2380 0.00 0.00 simplePreArcCount_pg
81	0.00 0.54 0.00 1931 0.00 0.00 addReadStart
82	0.00 0.54 0.00 1931 0.00 0.00 createArc
83	0.00 0.54 0.00 1931 0.00 0.00 incrementReadStartCount
84	0.00 0.54 0.00 1475 0.00 0.00 getTotalCoverage
85	0.00 0.54 0.00 1219 0.00 0.00 incrementAnnotationCoordinates
86	0.00 0.54 0.00 1209 0.00 0.00 getDestination
87	0.00 0.54 0.00 1190 0.00 0.00 isEligibleTip
88	0.00 0.54 0.00 1186 0.00 0.00 getTipLength
89	0.00 0.54 0.00 1184 0.00 0.00 arcCount
90	0.00 0.54 0.00 1180 0.00 0.00 getConnection
91	0.00 0.54 0.00 1180 0.00 0.00 getMarkedNodeList
92	0.00 0.54 0.00 1118 0.00 0.00 fh_extractmin
93	0.00 0.54 0.00 1118 0.00 0.00 removeNextNodeFromHeap
94	0.00 0.54 0.00 891 0.00 0.00 fh_insertkey
95	0.00 0.54 0.00 891 0.00 0.00 insertNodeIntoHeap
96	0.00 0.54 0.00 888 0.00 0.00 dfh_extractmin
97	0.00 0.54 0.00 888 0.00 0.00 removeNextNodeFromDHeap
98	0.00 0.54 0.00 819 0.00 0.00 fh_consolidate
99	0.00 0.54 0.00 595 0.00 0.00 projectFromNode
100	0.00 0.54 0.00 594 0.00 0.00 getOriginalVirtualCoverage
101	0.00 0.54 0.00 594 0.00 0.00 getVirtualCoverage
102	0.00 0.54 0.00 590 0.00 0.00 correctGraphLocally
103	0.00 0.54 0.00 590 0.00 0.00 expandLongNode
104	0.00 0.54 0.00 590 0.00 0.00 pushNeighbours
105	0.00 0.54 0.00 590 0.00 0.00 uniqueNodesConnect
106	0.00 0.54 0.00 588 0.00 0.00 readStartsAreActivated
107	0.00 0.54 0.00 584 0.00 0.00 readCoverage
108	0.00 0.54 0.00 574 0.00 0.00 getGap
109	0.00 0.54 0.00 445 0.00 0.00 getWordLength_pg
110	0.00 0.54 0.00 444 0.00 0.00 concatenatePreNodes
111	0.00 0.54 0.00 444 0.00 0.00 referenceMarkersAreActivated_pg
112	0.00 0.54 0.00 444 0.00 0.00 setPreNodeDescriptor_pg
113	0.00 0.54 0.00 310 0.00 0.00 destroyRecycleBin
114	0.00 0.54 0.00 308 0.00 0.00 newRecycleBin
115	0.00 0.54 0.00 299 0.00 0.00 destroyHeap
116	0.00 0.54 0.00 299 0.00 0.00 fh_deleteheap
117	0.00 0.54 0.00 299 0.00 0.00 fh_makekeyheap
118	0.00 0.54 0.00 299 0.00 0.00 newFibHeap
119	0.00 0.54 0.00 297 0.00 0.00 destroyNode
120	0.00 0.54 0.00 297 0.00 0.00 isUniqueSolexa
121	0.00 0.54 0.00 297 0.00 0.00 markerCount
122	0.00 0.54 0.00 297 0.00 0.00 setNodeStatus
123	0.00 0.54 0.00 297 0.00 0.00 setUniqueness
124	0.00 0.54 0.00 291 0.00 0.00 destroyTightString
125	0.00 0.54 0.00 291 0.00 0.00 newTightString
126	0.00 0.54 0.00 287 0.00 0.00 expandNode
127	0.00 0.54 0.00 287 0.00 0.00 exportLongNodeSequence
128	0.00 0.54 0.00 113 0.00 0.00 velvetLog
129	0.00 0.54 0.00 28 0.00 0.00 reallocOrExit4
130	0.00 0.54 0.00 8 0.00 0.00 renumberNodes
131	0.00 0.54 0.00 8 0.00 0.00 sortGapMarkers
132	0.00 0.54 0.00 7 0.00 0.00 concatenateGraph
133	0.00 0.54 0.00 6 0.00 0.00 getNextArc
134	0.00 0.54 0.00 4 0.00 0.00 projectFromSingleRead
135	0.00 0.54 0.00 4 0.00 0.00 resetNodeStatus
136	0.00 0.54 0.00 3 0.00 0.00 getInsertLength
137	0.00 0.54 0.00 3 0.00 0.00 getMultiplicity
138	0.00 0.54 0.00 3 0.00 0.00 setInsertLengths
139	0.00 0.54 0.00 2 0.00 0.00 clipTipsHard
140	0.00 0.54 0.00 2 0.00 0.00 concatenatePreGraph_pg
141	0.00 0.54 0.00 2 0.00 0.00 destroyDHeap
142	0.00 0.54 0.00 2 0.00 0.00 dfh_deleteheap
143	0.00 0.54 0.00 2 0.00 0.00 dfh_makekeyheap
144	0.00 0.54 0.00 2 0.00 0.00 exportGraph
145	0.00 0.54 0.00 2 0.00 0.00 getSequenceLengths
146	0.00 0.54 0.00 2 0.00 0.00 newDFibHeap
147	0.00 0.54 0.00 2 0.00 0.00 renumberPreNodes_pg
148	0.00 0.54 0.00 2 0.00 0.00 resetWordFilter
149	0.00 0.54 0.00 1 0.00 0.00 activateArcLookupTable
150	0.00 0.54 0.00 1 0.00 0.00 activateGapMarkers
151	0.00 0.54 0.00 1 0.00 0.00 activateReadStarts
152	0.00 0.54 0.00 1 0.00 0.00 allocateArc
153	0.00 0.54 0.00 1 0.00 0.00 allocateKmerOccurences
154	0.00 0.54 0.00 1 0.00 0.00 allocatePreNodeSpace_pg
155	0.00 0.54 0.00 1 0.00 0.00 buildScaffold
156	0.00 0.54 0.00 1 0.00 0.00 cleanScaffoldMemory
157	0.00 0.54 0.00 1 0.00 0.00 clipTips_pg
158	0.00 0.54 0.00 1 0.00 0.00 convertSequences
159	0.00 0.54 0.00 1 0.00 0.00 correctGraph
160	0.00 0.54 0.00 1 0.00 0.00 createAnalogousPreArc_pg
161	0.00 0.54 0.00 1 0.00 10.46 createPreNodes
162	0.00 0.54 0.00 1 0.00 0.00 createReadPairingArray
163	0.00 0.54 0.00 1 0.00 0.00 deactivateArcLookupTable
164	0.00 0.54 0.00 1 0.00 0.00 deactivateLocalCorrectionSettings
165	0.00 0.54 0.00 1 0.00 0.00 destroyAllPassageMarkers
166	0.00 0.54 0.00 1 0.00 0.00 destroyAllocArray
167	0.00 0.54 0.00 1 0.00 0.00 destroyArc
168	0.00 0.54 0.00 1 0.00 0.00 destroyGraph
169	0.00 0.54 0.00 1 0.00 0.00 destroyKmerOccurenceTable
170	0.00 0.54 0.00 1 0.00 0.00 destroyPreGraph_pg
171	0.00 0.54 0.00 1 0.00 0.00 destroyReadSet
172	0.00 0.54 0.00 1 0.00 0.00 destroyRoadMapArray
173	0.00 0.54 0.00 1 0.00 0.00 detachDubiousReads
174	0.00 0.54 0.00 1 0.00 0.00 dfh_insertkey
175	0.00 0.54 0.00 1 0.00 0.00 displayGeneralStatistics
176	0.00 0.54 0.00 1 0.00 0.00 emptyPreGraph_pg
177	0.00 0.54 0.00 1 0.00 0.00 exploitShortReadPairs
178	0.00 0.54 0.00 1 0.00 0.00 exportLongNodeSequences
179	0.00 0.54 0.00 1 0.00 0.00 exportPreGraph_pg
180	0.00 0.54 0.00 1 0.00 0.00 getArcBetweenNodes
181	0.00 0.54 0.00 1 0.00 529.54 importPreGraph
182	0.00 0.54 0.00 1 0.00 0.00 importReadSet
183	0.00 0.54 0.00 1 0.00 0.00 importRoadMapArray
184	0.00 0.54 0.00 1 0.00 0.00 insertNodeIntoDHeap
185	0.00 0.54 0.00 1 0.00 0.00 logFinalStats
186	0.00 0.54 0.00 1 0.00 0.00 logInstructions
187	0.00 0.54 0.00 1 0.00 0.00 n50
188	0.00 0.54 0.00 1 0.00 0.00 newAllocArray
189	0.00 0.54 0.00 1 0.00 0.00 newKmerOccurenceTable
190	0.00 0.54 0.00 1 0.00 10.46 newPreGraph_pg
191	0.00 0.54 0.00 1 0.00 0.00 newTightStringArrayFromStringArray
192	0.00 0.54 0.00 1 0.00 0.00 orderNodeReadStartArrays
193	0.00 0.54 0.00 1 0.00 0.00 pairedCategories
194	0.00 0.54 0.00 1 0.00 0.00 prepareGraphForLocalCorrections
195	0.00 0.54 0.00 1 0.00 0.00 readCoherentGraph
196	0.00 0.54 0.00 1 0.00 0.00 readPreGraphFile
197	0.00 0.54 0.00 1 0.00 461.54 referenceGraphKmers
198	0.00 0.54 0.00 1 0.00 0.00 removeHighCoverageNodes
199	0.00 0.54 0.00 1 0.00 0.00 removeLowCoverageNodesAndDenounceDubiousReads
200	0.00 0.54 0.00 1 0.00 0.00 removeLowCoverageReferenceNodes
201	0.00 0.54 0.00 1 0.00 0.00 removeLowLongCoverageNodesAndDenounceDubiousReads
202	0.00 0.54 0.00 1 0.00 0.00 removeUnreliableConnections
203	0.00 0.54 0.00 1 0.00 0.00 resetKeyFilter
204	0.00 0.54 0.00 1 0.00 0.00 setProgramName
205	0.00 0.54 0.00 1 0.00 0.00 usedReads
206
207	% the percentage of the total running time of the
208	time program used by this function.
209
210	cumulative a running sum of the number of seconds accounted
211	seconds for by this function and those listed above it.
212
213	self the number of seconds accounted for by this
214	seconds function alone. This is the major sort for this
215	listing.
216
217	calls the number of times this function was invoked, if
218	this function is profiled, else blank.
219
220	self the average number of milliseconds spent in this
221	ms/call function per call, if this function is profiled,
222	else blank.
223
224	total the average number of milliseconds spent in this
225	ms/call function and its descendents per call, if this
226	function is profiled, else blank.
227
228	name the name of the function. This is the minor sort
229	for this listing. The index shows the location of
230	the function in the gprof listing. If the index is
231	in parenthesis it shows where it would appear in
232	the gprof listing if it were to be printed.
233
234	Call graph (explanation follows)
235
236
237	granularity: each sample hit covers 4 byte(s) for 1.85% of 0.54 seconds
238
239	index % time self children called name
240	<spontaneous>
241	[1] 100.0 0.00 0.54 main [1]
242	0.00 0.53 1/1 importPreGraph [2]
243	0.00 0.01 1/1 newPreGraph_pg [8]
244	0.00 0.00 8/113 velvetLog [128]
245	0.00 0.00 6/3173 mallocOrExit3 [75]
246	0.00 0.00 3/3 setInsertLengths [138]
247	0.00 0.00 3/4295 getWordLength [64]
248	0.00 0.00 2/7 concatenateGraph [132]
249	0.00 0.00 2/2 exportGraph [144]
250	0.00 0.00 1/1 setProgramName [200]
251	0.00 0.00 1/1 logInstructions [184]
252	0.00 0.00 1/1 removeLowCoverageNodesAndDenounceDubiousReads [195]
253	0.00 0.00 1/1 removeLowLongCoverageNodesAndDenounceDubiousReads [197]
254	0.00 0.00 1/1 removeHighCoverageNodes [194]
255	0.00 0.00 1/2 clipTipsHard [139]
256	0.00 0.00 1/1 readCoherentGraph [192]
257	0.00 0.00 1/1 createReadPairingArray [161]
258	0.00 0.00 1/1 pairedCategories [190]
259	0.00 0.00 1/1 detachDubiousReads [172]
260	0.00 0.00 1/1 activateGapMarkers [150]
261	0.00 0.00 1/1 exploitShortReadPairs [176]
262	0.00 0.00 1/1 removeLowCoverageReferenceNodes [196]
263	0.00 0.00 1/1 exportLongNodeSequences [177]
264	0.00 0.00 1/1 displayGeneralStatistics [174]
265	0.00 0.00 1/1 logFinalStats [183]
266	0.00 0.00 1/1 destroyGraph [167]
267	0.00 0.00 1/1 destroyReadSet [170]
268	0.00 0.00 1/1 importRoadMapArray [181]
269	0.00 0.00 1/2 concatenatePreGraph_pg [140]
270	0.00 0.00 1/1 clipTips_pg [157]
271	0.00 0.00 1/1 exportPreGraph_pg [178]
272	0.00 0.00 1/1 destroyPreGraph_pg [169]
273	0.00 0.00 1/1 importReadSet [180]
274	0.00 0.00 1/1 convertSequences [158]
275	0.00 0.00 1/2 getSequenceLengths [145]
276	0.00 0.00 1/1 correctGraph [159]
277	-----------------------------------------------
278	0.00 0.53 1/1 main [1]
279	[2] 98.1 0.00 0.53 1 importPreGraph [2]
280	0.00 0.46 1/1 referenceGraphKmers [3]
281	0.02 0.02 318428/318428 findKmerInKmerOccurenceTable [5]
282	0.01 0.00 153040/153040 incrementVirtualCoverage [10]
283	0.01 0.00 1/1 createNodeReadStartArrays [12]
284	0.01 0.00 318428/998100 compareKmers [6]
285	0.00 0.00 382428/382428 getNucleotide [19]
286	0.00 0.00 382428/638766 pushNucleotide [14]
287	0.00 0.00 382428/453662 reversePushNucleotide [15]
288	0.00 0.00 327840/397647 getLength [17]
289	0.00 0.00 306080/306080 getKmerOccurenceNodeID [21]
290	0.00 0.00 306080/352440 getNodeInGraph [20]
291	0.00 0.00 154971/156159 getNodeStatus [22]
292	0.00 0.00 153040/153040 getKmerOccurencePosition [23]
293	0.00 0.00 153040/153040 incrementOriginalVirtualCoverage [24]
294	0.00 0.00 76201/118903 getNodeLength [25]
295	0.00 0.00 8000/10594 clearKmer [43]
296	0.00 0.00 7724/9792 setSingleNodeStatus [46]
297	0.00 0.00 4000/8000 getTightStringInArray [50]
298	0.00 0.00 4000/4295 getWordLength [64]
299	0.00 0.00 3862/5869 deallocatePointer [57]
300	0.00 0.00 3862/5940 allocatePointer [56]
301	0.00 0.00 1931/1931 createArc [82]
302	0.00 0.00 1931/1931 addReadStart [81]
303	0.00 0.00 1931/1931 incrementReadStartCount [83]
304	0.00 0.00 4/113 velvetLog [128]
305	0.00 0.00 1/1 readPreGraphFile [193]
306	0.00 0.00 1/17234 nodeCount [32]
307	0.00 0.00 1/4 resetNodeStatus [135]
308	0.00 0.00 1/588 readStartsAreActivated [106]
309	0.00 0.00 1/1 orderNodeReadStartArrays [189]
310	0.00 0.00 1/310 destroyRecycleBin [113]
311	0.00 0.00 1/1 destroyKmerOccurenceTable [168]
312	0.00 0.00 1/308 newRecycleBin [114]
313	0.00 0.00 1/1 activateReadStarts [151]
314	-----------------------------------------------
315	0.00 0.46 1/1 importPreGraph [2]
316	[3] 85.5 0.00 0.46 1 referenceGraphKmers [3]
317	0.45 0.00 1/1 sortKmerOccurenceTable [4]
318	0.00 0.01 66482/66482 recordKmerOccurence [13]
319	0.00 0.00 66482/998100 compareKmers [6]
320	0.00 0.00 71234/638766 pushNucleotide [14]
321	0.00 0.00 71234/453662 reversePushNucleotide [15]
322	0.00 0.00 33289/352440 getNodeInGraph [20]
323	0.00 0.00 33289/118903 getNodeLength [25]
324	0.00 0.00 594/10594 clearKmer [43]
325	0.00 0.00 2/113 velvetLog [128]
326	0.00 0.00 1/1 newKmerOccurenceTable [187]
327	0.00 0.00 1/1 allocateKmerOccurences [153]
328	-----------------------------------------------
329	0.45 0.00 1/1 referenceGraphKmers [3]
330	[4] 83.3 0.45 0.00 1 sortKmerOccurenceTable [4]
331	0.00 0.00 66482/384910 getKmerKey [18]
332	0.00 0.00 2/113 velvetLog [128]
333	-----------------------------------------------
334	0.02 0.02 318428/318428 importPreGraph [2]
335	[5] 7.1 0.02 0.02 318428 findKmerInKmerOccurenceTable [5]
336	0.02 0.00 613190/998100 compareKmers [6]
337	0.00 0.00 318428/384910 getKmerKey [18]
338	-----------------------------------------------
339	0.00 0.00 66482/998100 referenceGraphKmers [3]
340	0.01 0.00 318428/998100 importPreGraph [2]
341	0.02 0.00 613190/998100 findKmerInKmerOccurenceTable [5]
342	[6] 5.6 0.03 0.00 998100 compareKmers [6]
343	-----------------------------------------------
344	0.00 0.01 1/1 newPreGraph_pg [8]
345	[7] 1.9 0.00 0.01 1 createPreNodes [7]
346	0.01 0.00 3193/3193 addPreNodeToPreGraph_pg [9]
347	0.00 0.00 118590/638766 pushNucleotide [14]
348	0.00 0.00 89052/89052 getAnnotationLength [26]
349	0.00 0.00 10675/10675 getInsertionMarkerPosition [42]
350	0.00 0.00 7149/20844 getFinish [30]
351	0.00 0.00 7052/20582 getStart [31]
352	0.00 0.00 6045/13539 getPosition [36]
353	0.00 0.00 2462/3681 setFinishID [69]
354	0.00 0.00 2462/4924 setStartID [62]
355	0.00 0.00 2462/12310 getNextAnnotation [39]
356	0.00 0.00 2001/11194 sequenceCount_pg [40]
357	0.00 0.00 2000/10000 getRoadMapInArray [45]
358	0.00 0.00 2000/10000 getAnnotationCount [44]
359	0.00 0.00 2000/10594 clearKmer [43]
360	-----------------------------------------------
361	0.00 0.01 1/1 main [1]
362	[8] 1.9 0.00 0.01 1 newPreGraph_pg [8]
363	0.00 0.01 1/1 createPreNodes [7]
364	0.00 0.00 13741/13741 getAnnotSequenceID [35]
365	0.00 0.00 11216/15744 getPreNodeLength_pg [33]
366	0.00 0.00 9848/12310 getNextAnnotation [39]
367	0.00 0.00 9193/11194 sequenceCount_pg [40]
368	0.00 0.00 8000/10000 getRoadMapInArray [45]
369	0.00 0.00 8000/10000 getAnnotationCount [44]
370	0.00 0.00 7494/13539 getPosition [36]
371	0.00 0.00 6563/6563 getFinishID [53]
372	0.00 0.00 6089/6089 createPreArc_pg [54]
373	0.00 0.00 6026/20844 getFinish [30]
374	0.00 0.00 5941/20582 getStart [31]
375	0.00 0.00 5441/5441 getStartID [61]
376	0.00 0.00 5194/9287 preNodeCount_pg [47]
377	0.00 0.00 2462/4924 setStartID [62]
378	0.00 0.00 1219/1219 incrementAnnotationCoordinates [85]
379	0.00 0.00 1219/3681 setFinishID [69]
380	0.00 0.00 8/113 velvetLog [128]
381	0.00 0.00 4/4665 callocOrExit3 [63]
382	0.00 0.00 1/1 emptyPreGraph_pg [175]
383	0.00 0.00 1/1 allocatePreNodeSpace_pg [154]
384	0.00 0.00 1/1 destroyRoadMapArray [171]
385	-----------------------------------------------
386	0.01 0.00 3193/3193 createPreNodes [7]
387	[9] 1.9 0.01 0.00 3193 addPreNodeToPreGraph_pg [9]
388	0.00 0.00 3193/69675 copyKmers [11]
389	0.00 0.00 66514/638766 pushNucleotide [14]
390	0.00 0.00 51088/51088 popNucleotide [29]
391	0.00 0.00 3193/4665 callocOrExit3 [63]
392	-----------------------------------------------
393	0.01 0.00 153040/153040 importPreGraph [2]
394	[10] 1.9 0.01 0.00 153040 incrementVirtualCoverage [10]
395	-----------------------------------------------
396	0.00 0.00 3193/69675 addPreNodeToPreGraph_pg [9]
397	0.01 0.00 66482/69675 recordKmerOccurence [13]
398	[11] 1.9 0.01 0.00 69675 copyKmers [11]
399	-----------------------------------------------
400	0.01 0.00 1/1 importPreGraph [2]
401	[12] 1.9 0.01 0.00 1 createNodeReadStartArrays [12]
402	0.00 0.00 547/3173 mallocOrExit3 [75]
403	-----------------------------------------------
404	0.00 0.01 66482/66482 referenceGraphKmers [3]
405	[13] 1.8 0.00 0.01 66482 recordKmerOccurence [13]
406	0.01 0.00 66482/69675 copyKmers [11]
407	-----------------------------------------------
408	0.00 0.00 66514/638766 addPreNodeToPreGraph_pg [9]
409	0.00 0.00 71234/638766 referenceGraphKmers [3]
410	0.00 0.00 118590/638766 createPreNodes [7]
411	0.00 0.00 382428/638766 importPreGraph [2]
412	[14] 0.0 0.00 0.00 638766 pushNucleotide [14]
413	-----------------------------------------------
414	0.00 0.00 71234/453662 referenceGraphKmers [3]
415	0.00 0.00 382428/453662 importPreGraph [2]
416	[15] 0.0 0.00 0.00 453662 reversePushNucleotide [15]
417	-----------------------------------------------
418	0.00 0.00 2/421263 logFinalStats [183]
419	0.00 0.00 8/421263 logInstructions [184]
420	0.00 0.00 2979/421263 displayGeneralStatistics [174]
421	0.00 0.00 71829/421263 exportPreGraph_pg [178]
422	0.00 0.00 71993/421263 exportLongNodeSequence [127]
423	0.00 0.00 274452/421263 exportGraph [144]
424	[16] 0.0 0.00 0.00 421263 velvetFprintf [16]
425	-----------------------------------------------
426	0.00 0.00 4000/397647 getSequenceLengths [145]
427	0.00 0.00 65807/397647 exportLongNodeSequence [127]
428	0.00 0.00 327840/397647 importPreGraph [2]
429	[17] 0.0 0.00 0.00 397647 getLength [17]
430	-----------------------------------------------
431	0.00 0.00 66482/384910 sortKmerOccurenceTable [4]
432	0.00 0.00 318428/384910 findKmerInKmerOccurenceTable [5]
433	[18] 0.0 0.00 0.00 384910 getKmerKey [18]
434	-----------------------------------------------
435	0.00 0.00 382428/382428 importPreGraph [2]
436	[19] 0.0 0.00 0.00 382428 getNucleotide [19]
437	-----------------------------------------------
438	0.00 0.00 4/352440 projectFromSingleRead [134]
439	0.00 0.00 297/352440 usedReads [201]
440	0.00 0.00 297/352440 n50 [185]
441	0.00 0.00 297/352440 exportLongNodeSequences [177]
442	0.00 0.00 297/352440 displayGeneralStatistics [174]
443	0.00 0.00 297/352440 removeLowCoverageReferenceNodes [196]
444	0.00 0.00 297/352440 exploitShortReadPairs [176]
445	0.00 0.00 594/352440 logFinalStats [183]
446	0.00 0.00 594/352440 removeLowCoverageNodesAndDenounceDubiousReads [195]
447	0.00 0.00 594/352440 clipTipsHard [139]
448	0.00 0.00 595/352440 projectFromNode [99]
449	0.00 0.00 595/352440 removeUnreliableConnections [198]
450	0.00 0.00 891/352440 readCoherentGraph [192]
451	0.00 0.00 1784/352440 correctGraph [159]
452	0.00 0.00 2072/352440 concatenateGraph [132]
453	0.00 0.00 3566/352440 buildScaffold [155]
454	0.00 0.00 33289/352440 referenceGraphKmers [3]
455	0.00 0.00 306080/352440 importPreGraph [2]
456	[20] 0.0 0.00 0.00 352440 getNodeInGraph [20]
457	-----------------------------------------------
458	0.00 0.00 306080/306080 importPreGraph [2]
459	[21] 0.0 0.00 0.00 306080 getKmerOccurenceNodeID [21]
460	-----------------------------------------------
461	0.00 0.00 1/156159 pushNeighbours [104]
462	0.00 0.00 591/156159 correctGraphLocally [102]
463	0.00 0.00 596/156159 correctGraph [159]
464	0.00 0.00 154971/156159 importPreGraph [2]
465	[22] 0.0 0.00 0.00 156159 getNodeStatus [22]
466	-----------------------------------------------
467	0.00 0.00 153040/153040 importPreGraph [2]
468	[23] 0.0 0.00 0.00 153040 getKmerOccurencePosition [23]
469	-----------------------------------------------
470	0.00 0.00 153040/153040 importPreGraph [2]
471	[24] 0.0 0.00 0.00 153040 incrementOriginalVirtualCoverage [24]
472	-----------------------------------------------
473	0.00 0.00 1/118903 correctGraph [159]
474	0.00 0.00 297/118903 usedReads [201]
475	0.00 0.00 297/118903 exportLongNodeSequences [177]
476	0.00 0.00 297/118903 isUniqueSolexa [120]
477	0.00 0.00 574/118903 exportLongNodeSequence [127]
478	0.00 0.00 590/118903 pushNeighbours [104]
479	0.00 0.00 590/118903 expandLongNode [103]
480	0.00 0.00 601/118903 logFinalStats [183]
481	0.00 0.00 820/118903 n50 [185]
482	0.00 0.00 891/118903 removeLowCoverageReferenceNodes [196]
483	0.00 0.00 1188/118903 removeLowCoverageNodesAndDenounceDubiousReads [195]
484	0.00 0.00 1188/118903 getTipLength [88]
485	0.00 0.00 2079/118903 displayGeneralStatistics [174]
486	0.00 0.00 33289/118903 referenceGraphKmers [3]
487	0.00 0.00 76201/118903 importPreGraph [2]
488	[25] 0.0 0.00 0.00 118903 getNodeLength [25]
489	-----------------------------------------------
490	0.00 0.00 89052/89052 createPreNodes [7]
491	[26] 0.0 0.00 0.00 89052 getAnnotationLength [26]
492	-----------------------------------------------
493	0.00 0.00 70399/70399 exportLongNodeSequence [127]
494	[27] 0.0 0.00 0.00 70399 getNucleotideChar [27]
495	-----------------------------------------------
496	0.00 0.00 70399/70399 expandNode [126]
497	[28] 0.0 0.00 0.00 70399 writeNucleotideAtPosition [28]
498	-----------------------------------------------
499	0.00 0.00 51088/51088 addPreNodeToPreGraph_pg [9]
500	[29] 0.0 0.00 0.00 51088 popNucleotide [29]
501	-----------------------------------------------
502	0.00 0.00 6026/20844 newPreGraph_pg [8]
503	0.00 0.00 7149/20844 createPreNodes [7]
504	0.00 0.00 7669/20844 compareInsertionMarkers [238]
505	[30] 0.0 0.00 0.00 20844 getFinish [30]
506	-----------------------------------------------
507	0.00 0.00 5941/20582 newPreGraph_pg [8]
508	0.00 0.00 7052/20582 createPreNodes [7]
509	0.00 0.00 7589/20582 compareInsertionMarkers [238]
510	[31] 0.0 0.00 0.00 20582 getStart [31]
511	-----------------------------------------------
512	0.00 0.00 1/17234 importPreGraph [2]
513	0.00 0.00 3/17234 removeUnreliableConnections [198]
514	0.00 0.00 298/17234 usedReads [201]
515	0.00 0.00 298/17234 exportLongNodeSequences [177]
516	0.00 0.00 298/17234 displayGeneralStatistics [174]
517	0.00 0.00 298/17234 removeLowCoverageReferenceNodes [196]
518	0.00 0.00 299/17234 n50 [185]
519	0.00 0.00 299/17234 exploitShortReadPairs [176]
520	0.00 0.00 596/17234 removeLowCoverageNodesAndDenounceDubiousReads [195]
521	0.00 0.00 597/17234 logFinalStats [183]
522	0.00 0.00 597/17234 prepareGraphForLocalCorrections [191]
523	0.00 0.00 598/17234 clipTipsHard [139]
524	0.00 0.00 897/17234 readCoherentGraph [192]
525	0.00 0.00 1180/17234 getConnection [90]
526	0.00 0.00 1193/17234 buildScaffold [155]
527	0.00 0.00 2079/17234 concatenateGraph [132]
528	0.00 0.00 2360/17234 expandLongNode [103]
529	0.00 0.00 2360/17234 correctGraphLocally [102]
530	0.00 0.00 2983/17234 correctGraph [159]
531	[32] 0.0 0.00 0.00 17234 nodeCount [32]
532	-----------------------------------------------
533	0.00 0.00 1190/15744 isEligibleTip [87]
534	0.00 0.00 3338/15744 concatenatePreNodes [110]
535	0.00 0.00 11216/15744 newPreGraph_pg [8]
536	[33] 0.0 0.00 0.00 15744 getPreNodeLength_pg [33]
537	-----------------------------------------------
538	0.00 0.00 1090/14519 displayGeneralStatistics [174]
539	0.00 0.00 1911/14519 usedReads [201]
540	0.00 0.00 1914/14519 removeUnreliableConnections [198]
541	0.00 0.00 3862/14519 buildScaffold [155]
542	0.00 0.00 5742/14519 projectFromNode [99]
543	[34] 0.0 0.00 0.00 14519 getShortReadMarkerID [34]
544	-----------------------------------------------
545	0.00 0.00 13741/13741 newPreGraph_pg [8]
546	[35] 0.0 0.00 0.00 13741 getAnnotSequenceID [35]
547	-----------------------------------------------
548	0.00 0.00 6045/13539 createPreNodes [7]
549	0.00 0.00 7494/13539 newPreGraph_pg [8]
550	[36] 0.0 0.00 0.00 13539 getPosition [36]
551	-----------------------------------------------
552	0.00 0.00 1634/13140 concatenatePreGraph_pg [140]
553	0.00 0.00 2380/13140 isEligibleTip [87]
554	0.00 0.00 9126/13140 concatenatePreNodes [110]
555	[37] 0.0 0.00 0.00 13140 getPreArc_pg [37]
556	-----------------------------------------------
557	0.00 0.00 1190/12767 isEligibleTip [87]
558	0.00 0.00 11577/12767 concatenatePreNodes [110]
559	[38] 0.0 0.00 0.00 12767 getDestination_pg [38]
560	-----------------------------------------------
561	0.00 0.00 2462/12310 createPreNodes [7]
562	0.00 0.00 9848/12310 newPreGraph_pg [8]
563	[39] 0.0 0.00 0.00 12310 getNextAnnotation [39]
564	-----------------------------------------------
565	0.00 0.00 2001/11194 createPreNodes [7]
566	0.00 0.00 9193/11194 newPreGraph_pg [8]
567	[40] 0.0 0.00 0.00 11194 sequenceCount_pg [40]
568	-----------------------------------------------
569	0.00 0.00 1090/10691 displayGeneralStatistics [174]
570	0.00 0.00 1911/10691 usedReads [201]
571	0.00 0.00 1914/10691 projectFromNode [99]
572	0.00 0.00 1914/10691 removeUnreliableConnections [198]
573	0.00 0.00 3862/10691 buildScaffold [155]
574	[41] 0.0 0.00 0.00 10691 getShortReadMarkerAtIndex [41]
575	-----------------------------------------------
576	0.00 0.00 10675/10675 createPreNodes [7]
577	[42] 0.0 0.00 0.00 10675 getInsertionMarkerPosition [42]
578	-----------------------------------------------
579	0.00 0.00 594/10594 referenceGraphKmers [3]
580	0.00 0.00 2000/10594 createPreNodes [7]
581	0.00 0.00 8000/10594 importPreGraph [2]
582	[43] 0.0 0.00 0.00 10594 clearKmer [43]
583	-----------------------------------------------
584	0.00 0.00 2000/10000 createPreNodes [7]
585	0.00 0.00 8000/10000 newPreGraph_pg [8]
586	[44] 0.0 0.00 0.00 10000 getAnnotationCount [44]
587	-----------------------------------------------
588	0.00 0.00 2000/10000 createPreNodes [7]
589	0.00 0.00 8000/10000 newPreGraph_pg [8]
590	[45] 0.0 0.00 0.00 10000 getRoadMapInArray [45]
591	-----------------------------------------------
592	0.00 0.00 298/9792 correctGraph [159]
593	0.00 0.00 590/9792 pushNeighbours [104]
594	0.00 0.00 1180/9792 expandLongNode [103]
595	0.00 0.00 7724/9792 importPreGraph [2]
596	[46] 0.0 0.00 0.00 9792 setSingleNodeStatus [46]
597	-----------------------------------------------
598	0.00 0.00 601/9287 clipTips_pg [157]
599	0.00 0.00 3492/9287 concatenatePreGraph_pg [140]
600	0.00 0.00 5194/9287 newPreGraph_pg [8]
601	[47] 0.0 0.00 0.00 9287 preNodeCount_pg [47]
602	-----------------------------------------------
603	0.00 0.00 2080/8313 concatenatePreGraph_pg [140]
604	0.00 0.00 6233/8313 concatenatePreNodes [110]
605	[48] 0.0 0.00 0.00 8313 hasSinglePreArc_pg [48]
606	-----------------------------------------------
607	0.00 0.00 287/8272 exportLongNodeSequence [127]
608	0.00 0.00 297/8272 displayGeneralStatistics [174]
609	0.00 0.00 1180/8272 getConnection [90]
610	0.00 0.00 1788/8272 correctGraph [159]
611	0.00 0.00 2360/8272 expandLongNode [103]
612	0.00 0.00 2360/8272 correctGraphLocally [102]
613	[49] 0.0 0.00 0.00 8272 getNodeID [49]
614	-----------------------------------------------
615	0.00 0.00 4000/8000 getSequenceLengths [145]
616	0.00 0.00 4000/8000 importPreGraph [2]
617	[50] 0.0 0.00 0.00 8000 getTightStringInArray [50]
618	-----------------------------------------------
619	0.00 0.00 3562/7713 getTipLength [88]
620	0.00 0.00 4151/7713 concatenateGraph [132]
621	[51] 0.0 0.00 0.00 7713 simpleArcCount [51]
622	-----------------------------------------------
623	0.00 0.00 1/7103 pushNeighbours [104]
624	0.00 0.00 4/7103 projectFromSingleRead [134]
625	0.00 0.00 295/7103 exploitShortReadPairs [176]
626	0.00 0.00 295/7103 readCoherentGraph [192]
627	0.00 0.00 297/7103 displayGeneralStatistics [174]
628	0.00 0.00 574/7103 usedReads [201]
629	0.00 0.00 590/7103 expandLongNode [103]
630	0.00 0.00 594/7103 clipTipsHard [139]
631	0.00 0.00 2079/7103 concatenateGraph [132]
632	0.00 0.00 2374/7103 getTipLength [88]
633	[52] 0.0 0.00 0.00 7103 getTwinNode [52]
634	-----------------------------------------------
635	0.00 0.00 6563/6563 newPreGraph_pg [8]
636	[53] 0.0 0.00 0.00 6563 getFinishID [53]
637	-----------------------------------------------
638	0.00 0.00 6089/6089 newPreGraph_pg [8]
639	[54] 0.0 0.00 0.00 6089 createPreArc_pg [54]
640	0.00 0.00 2895/2896 allocArrayAllocate [77]
641	0.00 0.00 1/1 newAllocArray [186]
642	-----------------------------------------------
643	0.00 0.00 1/6010 logFinalStats [183]
644	0.00 0.00 1/6010 removeLowCoverageNodesAndDenounceDubiousReads [195]
645	0.00 0.00 2002/6010 usedReads [201]
646	0.00 0.00 4006/6010 buildScaffold [155]
647	[55] 0.0 0.00 0.00 6010 sequenceCount [55]
648	-----------------------------------------------
649	0.00 0.00 1/5940 allocateArc [152]
650	0.00 0.00 1/5940 correctGraph [159]
651	0.00 0.00 1/5940 dfh_insertkey [173]
652	0.00 0.00 590/5940 expandLongNode [103]
653	0.00 0.00 594/5940 readPreGraphFile [193]
654	0.00 0.00 891/5940 fh_insertkey [94]
655	0.00 0.00 3862/5940 importPreGraph [2]
656	[56] 0.0 0.00 0.00 5940 allocatePointer [56]
657	-----------------------------------------------
658	0.00 0.00 1/5869 correctGraph [159]
659	0.00 0.00 1/5869 dfh_extractmin [96]
660	0.00 0.00 297/5869 destroyGraph [167]
661	0.00 0.00 298/5869 destroyNode [119]
662	0.00 0.00 590/5869 expandLongNode [103]
663	0.00 0.00 820/5869 fh_extractmin [92]
664	0.00 0.00 3862/5869 importPreGraph [2]
665	[57] 0.0 0.00 0.00 5869 deallocatePointer [57]
666	-----------------------------------------------
667	0.00 0.00 1/5789 concatenatePreNodes [110]
668	0.00 0.00 5788/5789 removePreArcFromList_pg [59]
669	[58] 0.0 0.00 0.00 5789 getNextPreArc_pg [58]
670	-----------------------------------------------
671	0.00 0.00 5789/5789 destroyPreNode_pg [78]
672	[59] 0.0 0.00 0.00 5789 removePreArcFromList_pg [59]
673	0.00 0.00 5788/5789 getNextPreArc_pg [58]
674	-----------------------------------------------
675	0.00 0.00 14/5645 concatenateGraph [132]
676	0.00 0.00 590/5645 correctGraphLocally [102]
677	0.00 0.00 1180/5645 pushNeighbours [104]
678	0.00 0.00 1188/5645 getTipLength [88]
679	0.00 0.00 1188/5645 clipTipsHard [139]
680	0.00 0.00 1485/5645 correctGraph [159]
681	[60] 0.0 0.00 0.00 5645 getArc [60]
682	-----------------------------------------------
683	0.00 0.00 5441/5441 newPreGraph_pg [8]
684	[61] 0.0 0.00 0.00 5441 getStartID [61]
685	-----------------------------------------------
686	0.00 0.00 2462/4924 createPreNodes [7]
687	0.00 0.00 2462/4924 newPreGraph_pg [8]
688	[62] 0.0 0.00 0.00 4924 setStartID [62]
689	-----------------------------------------------
690	0.00 0.00 1/4665 newTightStringArrayFromStringArray [188]
691	0.00 0.00 1/4665 activateGapMarkers [150]
692	0.00 0.00 1/4665 activateArcLookupTable [149]
693	0.00 0.00 1/4665 usedReads [201]
694	0.00 0.00 1/4665 removeLowCoverageNodesAndDenounceDubiousReads [195]
695	0.00 0.00 1/4665 exploitShortReadPairs [176]
696	0.00 0.00 1/4665 removeUnreliableConnections [198]
697	0.00 0.00 1/4665 allocatePreNodeSpace_pg [154]
698	0.00 0.00 1/4665 allocateKmerOccurences [153]
699	0.00 0.00 1/4665 newKmerOccurenceTable [187]
700	0.00 0.00 2/4665 activateReadStarts [151]
701	0.00 0.00 2/4665 getSequenceLengths [145]
702	0.00 0.00 3/4665 importRoadMapArray [181]
703	0.00 0.00 4/4665 importReadSet [180]
704	0.00 0.00 4/4665 newPreGraph_pg [8]
705	0.00 0.00 5/4665 correctGraph [159]
706	0.00 0.00 10/4665 buildScaffold [155]
707	0.00 0.00 102/4665 prepareGraphForLocalCorrections [191]
708	0.00 0.00 291/4665 newTightString [125]
709	0.00 0.00 444/4665 concatenatePreNodes [110]
710	0.00 0.00 595/4665 readPreGraphFile [193]
711	0.00 0.00 3193/4665 addPreNodeToPreGraph_pg [9]
712	[63] 0.0 0.00 0.00 4665 callocOrExit3 [63]
713	-----------------------------------------------
714	0.00 0.00 1/4295 correctGraph [159]
715	0.00 0.00 1/4295 buildScaffold [155]
716	0.00 0.00 1/4295 prepareGraphForLocalCorrections [191]
717	0.00 0.00 2/4295 clipTipsHard [139]
718	0.00 0.00 3/4295 main [1]
719	0.00 0.00 287/4295 exportLongNodeSequence [127]
720	0.00 0.00 4000/4295 importPreGraph [2]
721	[64] 0.0 0.00 0.00 4295 getWordLength [64]
722	-----------------------------------------------
723	0.00 0.00 1/4137 uniqueNodesConnect [105]
724	0.00 0.00 2/4137 readCoherentGraph [192]
725	0.00 0.00 287/4137 usedReads [201]
726	0.00 0.00 297/4137 removeLowCoverageReferenceNodes [196]
727	0.00 0.00 584/4137 readCoverage [107]
728	0.00 0.00 590/4137 projectFromNode [99]
729	0.00 0.00 2376/4137 buildScaffold [155]
730	[65] 0.0 0.00 0.00 4137 getMarker [65]
731	-----------------------------------------------
732	0.00 0.00 598/4088 clipTips_pg [157]
733	0.00 0.00 3490/4088 concatenatePreGraph_pg [140]
734	[66] 0.0 0.00 0.00 4088 getPreNodeInPreGraph_pg [66]
735	-----------------------------------------------
736	0.00 0.00 1914/3845 projectFromNode [99]
737	0.00 0.00 1931/3845 buildScaffold [155]
738	[67] 0.0 0.00 0.00 3845 getShortReadMarkerOffset [67]
739	-----------------------------------------------
740	0.00 0.00 1914/3845 projectFromNode [99]
741	0.00 0.00 1931/3845 buildScaffold [155]
742	[68] 0.0 0.00 0.00 3845 getShortReadMarkerPosition [68]
743	-----------------------------------------------
744	0.00 0.00 1219/3681 newPreGraph_pg [8]
745	0.00 0.00 2462/3681 createPreNodes [7]
746	[69] 0.0 0.00 0.00 3681 setFinishID [69]
747	-----------------------------------------------
748	0.00 0.00 446/3341 concatenatePreGraph_pg [140]
749	0.00 0.00 2895/3341 concatenatePreNodes [110]
750	[70] 0.0 0.00 0.00 3341 getOtherEnd_pg [70]
751	-----------------------------------------------
752	0.00 0.00 446/3341 concatenatePreGraph_pg [140]
753	0.00 0.00 2895/3341 concatenatePreNodes [110]
754	[71] 0.0 0.00 0.00 3341 isLoop_pg [71]
755	-----------------------------------------------
756	0.00 0.00 3338/3338 concatenatePreNodes [110]
757	[72] 0.0 0.00 0.00 3338 appendDescriptors_pg [72]
758	-----------------------------------------------
759	0.00 0.00 297/3239 displayGeneralStatistics [174]
760	0.00 0.00 574/3239 usedReads [201]
761	0.00 0.00 590/3239 projectFromNode [99]
762	0.00 0.00 590/3239 removeUnreliableConnections [198]
763	0.00 0.00 1188/3239 buildScaffold [155]
764	[73] 0.0 0.00 0.00 3239 getNodeReadCount [73]
765	-----------------------------------------------
766	0.00 0.00 297/3239 displayGeneralStatistics [174]
767	0.00 0.00 574/3239 usedReads [201]
768	0.00 0.00 590/3239 projectFromNode [99]
769	0.00 0.00 590/3239 removeUnreliableConnections [198]
770	0.00 0.00 1188/3239 buildScaffold [155]
771	[74] 0.0 0.00 0.00 3239 getNodeReads [74]
772	-----------------------------------------------
773	0.00 0.00 1/3173 newTightStringArrayFromStringArray [188]
774	0.00 0.00 1/3173 readPreGraphFile [193]
775	0.00 0.00 1/3173 createReadPairingArray [161]
776	0.00 0.00 1/3173 logInstructions [184]
777	0.00 0.00 1/3173 emptyPreGraph_pg [175]
778	0.00 0.00 1/3173 newKmerOccurenceTable [187]
779	0.00 0.00 2/3173 logFinalStats [183]
780	0.00 0.00 2/3173 importRoadMapArray [181]
781	0.00 0.00 3/3173 prepareGraphForLocalCorrections [191]
782	0.00 0.00 3/3173 newAllocArray [186]
783	0.00 0.00 5/3173 correctGraph [159]
784	0.00 0.00 6/3173 main [1]
785	0.00 0.00 291/3173 newTightString [125]
786	0.00 0.00 308/3173 newRecycleBin [114]
787	0.00 0.00 547/3173 createNodeReadStartArrays [12]
788	0.00 0.00 2000/3173 importReadSet [180]
789	[75] 0.0 0.00 0.00 3173 mallocOrExit3 [75]
790	-----------------------------------------------
791	0.00 0.00 297/2966 exploitShortReadPairs [176]
792	0.00 0.00 590/2966 correctGraphLocally [102]
793	0.00 0.00 594/2966 projectFromNode [99]
794	0.00 0.00 594/2966 removeUnreliableConnections [198]
795	0.00 0.00 891/2966 readCoherentGraph [192]
796	[76] 0.0 0.00 0.00 2966 getUniqueness [76]
797	-----------------------------------------------
798	0.00 0.00 1/2896 createAnalogousPreArc_pg [160]
799	0.00 0.00 2895/2896 createPreArc_pg [54]
800	[77] 0.0 0.00 0.00 2896 allocArrayAllocate [77]
801	-----------------------------------------------
802	0.00 0.00 2/2896 clipTips_pg [157]
803	0.00 0.00 2894/2896 concatenatePreNodes [110]
804	[78] 0.0 0.00 0.00 2896 destroyPreNode_pg [78]
805	0.00 0.00 5789/5789 removePreArcFromList_pg [59]
806	0.00 0.00 2895/2895 allocArrayFree [79]
807	-----------------------------------------------
808	0.00 0.00 2895/2895 destroyPreNode_pg [78]
809	[79] 0.0 0.00 0.00 2895 allocArrayFree [79]
810	-----------------------------------------------
811	0.00 0.00 2380/2380 isEligibleTip [87]
812	[80] 0.0 0.00 0.00 2380 simplePreArcCount_pg [80]
813	-----------------------------------------------
814	0.00 0.00 1931/1931 importPreGraph [2]
815	[81] 0.0 0.00 0.00 1931 addReadStart [81]
816	-----------------------------------------------
817	0.00 0.00 1931/1931 importPreGraph [2]
818	[82] 0.0 0.00 0.00 1931 createArc [82]
819	0.00 0.00 1/1 allocateArc [152]
820	-----------------------------------------------
821	0.00 0.00 1931/1931 importPreGraph [2]
822	[83] 0.0 0.00 0.00 1931 incrementReadStartCount [83]
823	-----------------------------------------------
824	0.00 0.00 287/1475 exportLongNodeSequence [127]
825	0.00 0.00 297/1475 removeLowCoverageReferenceNodes [196]
826	0.00 0.00 297/1475 isUniqueSolexa [120]
827	0.00 0.00 594/1475 removeLowCoverageNodesAndDenounceDubiousReads [195]
828	[84] 0.0 0.00 0.00 1475 getTotalCoverage [84]
829	-----------------------------------------------
830	0.00 0.00 1219/1219 newPreGraph_pg [8]
831	[85] 0.0 0.00 0.00 1219 incrementAnnotationCoordinates [85]
832	-----------------------------------------------
833	0.00 0.00 2/1209 pushNeighbours [104]
834	0.00 0.00 2/1209 correctGraphLocally [102]
835	0.00 0.00 3/1209 correctGraph [159]
836	0.00 0.00 14/1209 concatenateGraph [132]
837	0.00 0.00 1188/1209 getTipLength [88]
838	[86] 0.0 0.00 0.00 1209 getDestination [86]
839	-----------------------------------------------
840	0.00 0.00 1190/1190 clipTips_pg [157]
841	[87] 0.0 0.00 0.00 1190 isEligibleTip [87]
842	0.00 0.00 2380/13140 getPreArc_pg [37]
843	0.00 0.00 2380/2380 simplePreArcCount_pg [80]
844	0.00 0.00 1190/15744 getPreNodeLength_pg [33]
845	0.00 0.00 1190/12767 getDestination_pg [38]
846	-----------------------------------------------
847	0.00 0.00 1186/1186 clipTipsHard [139]
848	[88] 0.0 0.00 0.00 1186 getTipLength [88]
849	0.00 0.00 3562/7713 simpleArcCount [51]
850	0.00 0.00 2374/7103 getTwinNode [52]
851	0.00 0.00 1188/118903 getNodeLength [25]
852	0.00 0.00 1188/5645 getArc [60]
853	0.00 0.00 1188/1209 getDestination [86]
854	-----------------------------------------------
855	0.00 0.00 590/1184 uniqueNodesConnect [105]
856	0.00 0.00 594/1184 displayGeneralStatistics [174]
857	[89] 0.0 0.00 0.00 1184 arcCount [89]
858	-----------------------------------------------
859	0.00 0.00 1180/1180 expandLongNode [103]
860	[90] 0.0 0.00 0.00 1180 getConnection [90]
861	0.00 0.00 1180/8272 getNodeID [49]
862	0.00 0.00 1180/17234 nodeCount [32]
863	-----------------------------------------------
864	0.00 0.00 1180/1180 correctGraphLocally [102]
865	[91] 0.0 0.00 0.00 1180 getMarkedNodeList [91]
866	-----------------------------------------------
867	0.00 0.00 226/1118 n50 [185]
868	0.00 0.00 892/1118 correctGraph [159]
869	[92] 0.0 0.00 0.00 1118 fh_extractmin [92]
870	0.00 0.00 820/5869 deallocatePointer [57]
871	0.00 0.00 819/819 fh_consolidate [98]
872	-----------------------------------------------
873	0.00 0.00 226/1118 n50 [185]
874	0.00 0.00 892/1118 correctGraph [159]
875	[93] 0.0 0.00 0.00 1118 removeNextNodeFromHeap [93]
876	-----------------------------------------------
877	0.00 0.00 297/891 n50 [185]
878	0.00 0.00 594/891 correctGraph [159]
879	[94] 0.0 0.00 0.00 891 fh_insertkey [94]
880	0.00 0.00 891/5940 allocatePointer [56]
881	-----------------------------------------------
882	0.00 0.00 297/891 n50 [185]
883	0.00 0.00 594/891 correctGraph [159]
884	[95] 0.0 0.00 0.00 891 insertNodeIntoHeap [95]
885	-----------------------------------------------
886	0.00 0.00 298/888 correctGraph [159]
887	0.00 0.00 590/888 correctGraphLocally [102]
888	[96] 0.0 0.00 0.00 888 dfh_extractmin [96]
889	0.00 0.00 1/5869 deallocatePointer [57]
890	-----------------------------------------------
891	0.00 0.00 298/888 correctGraph [159]
892	0.00 0.00 590/888 correctGraphLocally [102]
893	[97] 0.0 0.00 0.00 888 removeNextNodeFromDHeap [97]
894	-----------------------------------------------
895	0.00 0.00 819/819 fh_extractmin [92]
896	[98] 0.0 0.00 0.00 819 fh_consolidate [98]
897	-----------------------------------------------
898	0.00 0.00 595/595 buildScaffold [155]
899	[99] 0.0 0.00 0.00 595 projectFromNode [99]
900	0.00 0.00 5742/14519 getShortReadMarkerID [34]
901	0.00 0.00 1914/10691 getShortReadMarkerAtIndex [41]
902	0.00 0.00 1914/3845 getShortReadMarkerPosition [68]
903	0.00 0.00 1914/3845 getShortReadMarkerOffset [67]
904	0.00 0.00 595/352440 getNodeInGraph [20]
905	0.00 0.00 594/2966 getUniqueness [76]
906	0.00 0.00 590/3239 getNodeReads [74]
907	0.00 0.00 590/3239 getNodeReadCount [73]
908	0.00 0.00 590/4137 getMarker [65]
909	0.00 0.00 4/4 projectFromSingleRead [134]
910	-----------------------------------------------
911	0.00 0.00 594/594 displayGeneralStatistics [174]
912	[100] 0.0 0.00 0.00 594 getOriginalVirtualCoverage [100]
913	-----------------------------------------------
914	0.00 0.00 594/594 displayGeneralStatistics [174]
915	[101] 0.0 0.00 0.00 594 getVirtualCoverage [101]
916	-----------------------------------------------
917	0.00 0.00 590/590 expandLongNode [103]
918	[102] 0.0 0.00 0.00 590 correctGraphLocally [102]
919	0.00 0.00 2360/8272 getNodeID [49]
920	0.00 0.00 2360/17234 nodeCount [32]
921	0.00 0.00 1180/1180 getMarkedNodeList [91]
922	0.00 0.00 591/156159 getNodeStatus [22]
923	0.00 0.00 590/5645 getArc [60]
924	0.00 0.00 590/888 dfh_extractmin [96]
925	0.00 0.00 590/888 removeNextNodeFromDHeap [97]
926	0.00 0.00 590/2966 getUniqueness [76]
927	0.00 0.00 2/1209 getDestination [86]
928	0.00 0.00 1/6 getNextArc [133]
929	-----------------------------------------------
930	0.00 0.00 590/590 exploitShortReadPairs [176]
931	[103] 0.0 0.00 0.00 590 expandLongNode [103]
932	0.00 0.00 2360/8272 getNodeID [49]
933	0.00 0.00 2360/17234 nodeCount [32]
934	0.00 0.00 1180/9792 setSingleNodeStatus [46]
935	0.00 0.00 1180/1180 getConnection [90]
936	0.00 0.00 590/118903 getNodeLength [25]
937	0.00 0.00 590/5940 allocatePointer [56]
938	0.00 0.00 590/7103 getTwinNode [52]
939	0.00 0.00 590/590 correctGraphLocally [102]
940	0.00 0.00 590/590 pushNeighbours [104]
941	0.00 0.00 590/5869 deallocatePointer [57]
942	0.00 0.00 1/308 newRecycleBin [114]
943	-----------------------------------------------
944	0.00 0.00 590/590 expandLongNode [103]
945	[104] 0.0 0.00 0.00 590 pushNeighbours [104]
946	0.00 0.00 1180/5645 getArc [60]
947	0.00 0.00 590/118903 getNodeLength [25]
948	0.00 0.00 590/9792 setSingleNodeStatus [46]
949	0.00 0.00 2/1209 getDestination [86]
950	0.00 0.00 2/6 getNextArc [133]
951	0.00 0.00 1/7103 getTwinNode [52]
952	0.00 0.00 1/156159 getNodeStatus [22]
953	-----------------------------------------------
954	0.00 0.00 590/590 readCoherentGraph [192]
955	[105] 0.0 0.00 0.00 590 uniqueNodesConnect [105]
956	0.00 0.00 590/1184 arcCount [89]
957	0.00 0.00 1/4137 getMarker [65]
958	-----------------------------------------------
959	0.00 0.00 1/588 removeLowLongCoverageNodesAndDenounceDubiousReads [197]
960	0.00 0.00 1/588 removeLowCoverageNodesAndDenounceDubiousReads [195]
961	0.00 0.00 1/588 exploitShortReadPairs [176]
962	0.00 0.00 1/588 importPreGraph [2]
963	0.00 0.00 287/588 usedReads [201]
964	0.00 0.00 297/588 displayGeneralStatistics [174]
965	[106] 0.0 0.00 0.00 588 readStartsAreActivated [106]
966	-----------------------------------------------
967	0.00 0.00 287/584 exportLongNodeSequence [127]
968	0.00 0.00 297/584 displayGeneralStatistics [174]
969	[107] 0.0 0.00 0.00 584 readCoverage [107]
970	0.00 0.00 584/4137 getMarker [65]
971	-----------------------------------------------
972	0.00 0.00 574/574 exportLongNodeSequence [127]
973	[108] 0.0 0.00 0.00 574 getGap [108]
974	-----------------------------------------------
975	0.00 0.00 1/445 clipTips_pg [157]
976	0.00 0.00 444/445 concatenatePreNodes [110]
977	[109] 0.0 0.00 0.00 445 getWordLength_pg [109]
978	-----------------------------------------------
979	0.00 0.00 444/444 concatenatePreGraph_pg [140]
980	[110] 0.0 0.00 0.00 444 concatenatePreNodes [110]
981	0.00 0.00 11577/12767 getDestination_pg [38]
982	0.00 0.00 9126/13140 getPreArc_pg [37]
983	0.00 0.00 6233/8313 hasSinglePreArc_pg [48]
984	0.00 0.00 3338/15744 getPreNodeLength_pg [33]
985	0.00 0.00 3338/3338 appendDescriptors_pg [72]
986	0.00 0.00 2895/3341 getOtherEnd_pg [70]
987	0.00 0.00 2895/3341 isLoop_pg [71]
988	0.00 0.00 2894/2896 destroyPreNode_pg [78]
989	0.00 0.00 444/445 getWordLength_pg [109]
990	0.00 0.00 444/444 referenceMarkersAreActivated_pg [111]
991	0.00 0.00 444/4665 callocOrExit3 [63]
992	0.00 0.00 444/444 setPreNodeDescriptor_pg [112]
993	0.00 0.00 1/5789 getNextPreArc_pg [58]
994	0.00 0.00 1/1 createAnalogousPreArc_pg [160]
995	-----------------------------------------------
996	0.00 0.00 444/444 concatenatePreNodes [110]
997	[111] 0.0 0.00 0.00 444 referenceMarkersAreActivated_pg [111]
998	-----------------------------------------------
999	0.00 0.00 444/444 concatenatePreNodes [110]
1000	[112] 0.0 0.00 0.00 444 setPreNodeDescriptor_pg [112]
1001	-----------------------------------------------
1002	0.00 0.00 1/310 correctGraph [159]
1003	0.00 0.00 1/310 exploitShortReadPairs [176]
1004	0.00 0.00 1/310 cleanScaffoldMemory [156]
1005	0.00 0.00 1/310 buildScaffold [155]
1006	0.00 0.00 1/310 importPreGraph [2]
1007	0.00 0.00 1/310 readCoherentGraph [192]
1008	0.00 0.00 2/310 dfh_deleteheap [142]
1009	0.00 0.00 3/310 destroyGraph [167]
1010	0.00 0.00 299/310 fh_deleteheap [116]
1011	[113] 0.0 0.00 0.00 310 destroyRecycleBin [113]
1012	-----------------------------------------------
1013	0.00 0.00 1/308 activateGapMarkers [150]
1014	0.00 0.00 1/308 allocateArc [152]
1015	0.00 0.00 1/308 readPreGraphFile [193]
1016	0.00 0.00 1/308 correctGraph [159]
1017	0.00 0.00 1/308 expandLongNode [103]
1018	0.00 0.00 1/308 importPreGraph [2]
1019	0.00 0.00 1/308 readCoherentGraph [192]
1020	0.00 0.00 2/308 dfh_makekeyheap [143]
1021	0.00 0.00 299/308 fh_makekeyheap [117]
1022	[114] 0.0 0.00 0.00 308 newRecycleBin [114]
1023	0.00 0.00 308/3173 mallocOrExit3 [75]
1024	-----------------------------------------------
1025	0.00 0.00 1/299 n50 [185]
1026	0.00 0.00 298/299 correctGraph [159]
1027	[115] 0.0 0.00 0.00 299 destroyHeap [115]
1028	-----------------------------------------------
1029	0.00 0.00 1/299 n50 [185]
1030	0.00 0.00 298/299 correctGraph [159]
1031	[116] 0.0 0.00 0.00 299 fh_deleteheap [116]
1032	0.00 0.00 299/310 destroyRecycleBin [113]
1033	-----------------------------------------------
1034	0.00 0.00 299/299 newFibHeap [118]
1035	[117] 0.0 0.00 0.00 299 fh_makekeyheap [117]
1036	0.00 0.00 299/308 newRecycleBin [114]
1037	-----------------------------------------------
1038	0.00 0.00 1/299 n50 [185]
1039	0.00 0.00 298/299 correctGraph [159]
1040	[118] 0.0 0.00 0.00 299 newFibHeap [118]
1041	0.00 0.00 299/299 fh_makekeyheap [117]
1042	-----------------------------------------------
1043	0.00 0.00 297/297 destroyGraph [167]
1044	[119] 0.0 0.00 0.00 297 destroyNode [119]
1045	0.00 0.00 298/5869 deallocatePointer [57]
1046	0.00 0.00 1/1 destroyArc [166]
1047	-----------------------------------------------
1048	0.00 0.00 297/297 readCoherentGraph [192]
1049	[120] 0.0 0.00 0.00 297 isUniqueSolexa [120]
1050	0.00 0.00 297/118903 getNodeLength [25]
1051	0.00 0.00 297/1475 getTotalCoverage [84]
1052	-----------------------------------------------
1053	0.00 0.00 297/297 displayGeneralStatistics [174]
1054	[121] 0.0 0.00 0.00 297 markerCount [121]
1055	-----------------------------------------------
1056	0.00 0.00 297/297 correctGraph [159]
1057	[122] 0.0 0.00 0.00 297 setNodeStatus [122]
1058	-----------------------------------------------
1059	0.00 0.00 297/297 readCoherentGraph [192]
1060	[123] 0.0 0.00 0.00 297 setUniqueness [123]
1061	-----------------------------------------------
1062	0.00 0.00 2/291 correctGraph [159]
1063	0.00 0.00 2/291 deactivateLocalCorrectionSettings [163]
1064	0.00 0.00 287/291 exportLongNodeSequences [177]
1065	[124] 0.0 0.00 0.00 291 destroyTightString [124]
1066	-----------------------------------------------
1067	0.00 0.00 2/291 correctGraph [159]
1068	0.00 0.00 2/291 prepareGraphForLocalCorrections [191]
1069	0.00 0.00 287/291 expandNode [126]
1070	[125] 0.0 0.00 0.00 291 newTightString [125]
1071	0.00 0.00 291/3173 mallocOrExit3 [75]
1072	0.00 0.00 291/4665 callocOrExit3 [63]
1073	-----------------------------------------------
1074	0.00 0.00 287/287 exportLongNodeSequence [127]
1075	[126] 0.0 0.00 0.00 287 expandNode [126]
1076	0.00 0.00 70399/70399 writeNucleotideAtPosition [28]
1077	0.00 0.00 287/291 newTightString [125]
1078	-----------------------------------------------
1079	0.00 0.00 287/287 exportLongNodeSequences [177]
1080	[127] 0.0 0.00 0.00 287 exportLongNodeSequence [127]
1081	0.00 0.00 71993/421263 velvetFprintf [16]
1082	0.00 0.00 70399/70399 getNucleotideChar [27]
1083	0.00 0.00 65807/397647 getLength [17]
1084	0.00 0.00 574/118903 getNodeLength [25]
1085	0.00 0.00 574/574 getGap [108]
1086	0.00 0.00 287/4295 getWordLength [64]
1087	0.00 0.00 287/8272 getNodeID [49]
1088	0.00 0.00 287/287 expandNode [126]
1089	0.00 0.00 287/1475 getTotalCoverage [84]
1090	0.00 0.00 287/584 readCoverage [107]
1091	-----------------------------------------------
1092	0.00 0.00 1/113 activateArcLookupTable [149]
1093	0.00 0.00 1/113 exportLongNodeSequences [177]
1094	0.00 0.00 1/113 displayGeneralStatistics [174]
1095	0.00 0.00 1/113 removeLowCoverageReferenceNodes [196]
1096	0.00 0.00 1/113 deactivateLocalCorrectionSettings [163]
1097	0.00 0.00 1/113 prepareGraphForLocalCorrections [191]
1098	0.00 0.00 1/113 exportPreGraph_pg [178]
1099	0.00 0.00 2/113 exportGraph [144]
1100	0.00 0.00 2/113 readPreGraphFile [193]
1101	0.00 0.00 2/113 exploitShortReadPairs [176]
1102	0.00 0.00 2/113 referenceGraphKmers [3]
1103	0.00 0.00 2/113 importRoadMapArray [181]
1104	0.00 0.00 2/113 concatenatePreGraph_pg [140]
1105	0.00 0.00 2/113 sortKmerOccurenceTable [4]
1106	0.00 0.00 3/113 removeLowCoverageNodesAndDenounceDubiousReads [195]
1107	0.00 0.00 3/113 importReadSet [180]
1108	0.00 0.00 4/113 importPreGraph [2]
1109	0.00 0.00 4/113 clipTips_pg [157]
1110	0.00 0.00 5/113 readCoherentGraph [192]
1111	0.00 0.00 6/113 clipTipsHard [139]
1112	0.00 0.00 6/113 renumberPreNodes_pg [147]
1113	0.00 0.00 7/113 concatenateGraph [132]
1114	0.00 0.00 7/113 correctGraph [159]
1115	0.00 0.00 7/113 buildScaffold [155]
1116	0.00 0.00 8/113 main [1]
1117	0.00 0.00 8/113 newPreGraph_pg [8]
1118	0.00 0.00 24/113 renumberNodes [130]
1119	[128] 0.0 0.00 0.00 113 velvetLog [128]
1120	-----------------------------------------------
1121	0.00 0.00 2/28 renumberPreNodes_pg [147]
1122	0.00 0.00 26/28 renumberNodes [130]
1123	[129] 0.0 0.00 0.00 28 reallocOrExit4 [129]
1124	-----------------------------------------------
1125	0.00 0.00 1/8 readCoherentGraph [192]
1126	0.00 0.00 7/8 concatenateGraph [132]
1127	[130] 0.0 0.00 0.00 8 renumberNodes [130]
1128	0.00 0.00 26/28 reallocOrExit4 [129]
1129	0.00 0.00 24/113 velvetLog [128]
1130	-----------------------------------------------
1131	0.00 0.00 1/8 exploitShortReadPairs [176]
1132	0.00 0.00 7/8 concatenateGraph [132]
1133	[131] 0.0 0.00 0.00 8 sortGapMarkers [131]
1134	-----------------------------------------------
1135	0.00 0.00 1/7 correctGraph [159]
1136	0.00 0.00 2/7 main [1]
1137	0.00 0.00 2/7 removeLowCoverageNodesAndDenounceDubiousReads [195]
1138	0.00 0.00 2/7 clipTipsHard [139]
1139	[132] 0.0 0.00 0.00 7 concatenateGraph [132]
1140	0.00 0.00 4151/7713 simpleArcCount [51]
1141	0.00 0.00 2079/17234 nodeCount [32]
1142	0.00 0.00 2079/7103 getTwinNode [52]
1143	0.00 0.00 2072/352440 getNodeInGraph [20]
1144	0.00 0.00 14/5645 getArc [60]
1145	0.00 0.00 14/1209 getDestination [86]
1146	0.00 0.00 7/113 velvetLog [128]
1147	0.00 0.00 7/8 renumberNodes [130]
1148	0.00 0.00 7/8 sortGapMarkers [131]
1149	-----------------------------------------------
1150	0.00 0.00 1/6 correctGraphLocally [102]
1151	0.00 0.00 2/6 pushNeighbours [104]
1152	0.00 0.00 3/6 correctGraph [159]
1153	[133] 0.0 0.00 0.00 6 getNextArc [133]
1154	-----------------------------------------------
1155	0.00 0.00 4/4 projectFromNode [99]
1156	[134] 0.0 0.00 0.00 4 projectFromSingleRead [134]
1157	0.00 0.00 4/352440 getNodeInGraph [20]
1158	0.00 0.00 4/7103 getTwinNode [52]
1159	-----------------------------------------------
1160	0.00 0.00 1/4 correctGraph [159]
1161	0.00 0.00 1/4 exploitShortReadPairs [176]
1162	0.00 0.00 1/4 importPreGraph [2]
1163	0.00 0.00 1/4 readCoherentGraph [192]
1164	[135] 0.0 0.00 0.00 4 resetNodeStatus [135]
1165	-----------------------------------------------
1166	0.00 0.00 3/3 removeUnreliableConnections [198]
1167	[136] 0.0 0.00 0.00 3 getInsertLength [136]
1168	-----------------------------------------------
1169	0.00 0.00 3/3 correctGraph [159]
1170	[137] 0.0 0.00 0.00 3 getMultiplicity [137]
1171	-----------------------------------------------
1172	0.00 0.00 3/3 main [1]
1173	[138] 0.0 0.00 0.00 3 setInsertLengths [138]
1174	-----------------------------------------------
1175	0.00 0.00 1/2 main [1]
1176	0.00 0.00 1/2 correctGraph [159]
1177	[139] 0.0 0.00 0.00 2 clipTipsHard [139]
1178	0.00 0.00 1188/5645 getArc [60]
1179	0.00 0.00 1186/1186 getTipLength [88]
1180	0.00 0.00 598/17234 nodeCount [32]
1181	0.00 0.00 594/352440 getNodeInGraph [20]
1182	0.00 0.00 594/7103 getTwinNode [52]
1183	0.00 0.00 6/113 velvetLog [128]
1184	0.00 0.00 2/4295 getWordLength [64]
1185	0.00 0.00 2/7 concatenateGraph [132]
1186	-----------------------------------------------
1187	0.00 0.00 1/2 main [1]
1188	0.00 0.00 1/2 clipTips_pg [157]
1189	[140] 0.0 0.00 0.00 2 concatenatePreGraph_pg [140]
1190	0.00 0.00 3492/9287 preNodeCount_pg [47]
1191	0.00 0.00 3490/4088 getPreNodeInPreGraph_pg [66]
1192	0.00 0.00 2080/8313 hasSinglePreArc_pg [48]
1193	0.00 0.00 1634/13140 getPreArc_pg [37]
1194	0.00 0.00 446/3341 getOtherEnd_pg [70]
1195	0.00 0.00 446/3341 isLoop_pg [71]
1196	0.00 0.00 444/444 concatenatePreNodes [110]
1197	0.00 0.00 2/113 velvetLog [128]
1198	0.00 0.00 2/2 renumberPreNodes_pg [147]
1199	-----------------------------------------------
1200	0.00 0.00 1/2 correctGraph [159]
1201	0.00 0.00 1/2 deactivateLocalCorrectionSettings [163]
1202	[141] 0.0 0.00 0.00 2 destroyDHeap [141]
1203	-----------------------------------------------
1204	0.00 0.00 1/2 correctGraph [159]
1205	0.00 0.00 1/2 deactivateLocalCorrectionSettings [163]
1206	[142] 0.0 0.00 0.00 2 dfh_deleteheap [142]
1207	0.00 0.00 2/310 destroyRecycleBin [113]
1208	-----------------------------------------------
1209	0.00 0.00 2/2 newDFibHeap [146]
1210	[143] 0.0 0.00 0.00 2 dfh_makekeyheap [143]
1211	0.00 0.00 2/308 newRecycleBin [114]
1212	-----------------------------------------------
1213	0.00 0.00 2/2 main [1]
1214	[144] 0.0 0.00 0.00 2 exportGraph [144]
1215	0.00 0.00 274452/421263 velvetFprintf [16]
1216	0.00 0.00 2/113 velvetLog [128]
1217	-----------------------------------------------
1218	0.00 0.00 1/2 main [1]
1219	0.00 0.00 1/2 buildScaffold [155]
1220	[145] 0.0 0.00 0.00 2 getSequenceLengths [145]
1221	0.00 0.00 4000/8000 getTightStringInArray [50]
1222	0.00 0.00 4000/397647 getLength [17]
1223	0.00 0.00 2/4665 callocOrExit3 [63]
1224	-----------------------------------------------
1225	0.00 0.00 1/2 correctGraph [159]
1226	0.00 0.00 1/2 prepareGraphForLocalCorrections [191]
1227	[146] 0.0 0.00 0.00 2 newDFibHeap [146]
1228	0.00 0.00 2/2 dfh_makekeyheap [143]
1229	-----------------------------------------------
1230	0.00 0.00 2/2 concatenatePreGraph_pg [140]
1231	[147] 0.0 0.00 0.00 2 renumberPreNodes_pg [147]
1232	0.00 0.00 6/113 velvetLog [128]
1233	0.00 0.00 2/28 reallocOrExit4 [129]
1234	-----------------------------------------------
1235	0.00 0.00 1/2 readPreGraphFile [193]
1236	0.00 0.00 1/2 importRoadMapArray [181]
1237	[148] 0.0 0.00 0.00 2 resetWordFilter [148]
1238	-----------------------------------------------
1239	0.00 0.00 1/1 correctGraph [159]
1240	[149] 0.0 0.00 0.00 1 activateArcLookupTable [149]
1241	0.00 0.00 1/113 velvetLog [128]
1242	0.00 0.00 1/4665 callocOrExit3 [63]
1243	-----------------------------------------------
1244	0.00 0.00 1/1 main [1]
1245	[150] 0.0 0.00 0.00 1 activateGapMarkers [150]
1246	0.00 0.00 1/4665 callocOrExit3 [63]
1247	0.00 0.00 1/308 newRecycleBin [114]
1248	-----------------------------------------------
1249	0.00 0.00 1/1 importPreGraph [2]
1250	[151] 0.0 0.00 0.00 1 activateReadStarts [151]
1251	0.00 0.00 2/4665 callocOrExit3 [63]
1252	-----------------------------------------------
1253	0.00 0.00 1/1 createArc [82]
1254	[152] 0.0 0.00 0.00 1 allocateArc [152]
1255	0.00 0.00 1/308 newRecycleBin [114]
1256	0.00 0.00 1/5940 allocatePointer [56]
1257	-----------------------------------------------
1258	0.00 0.00 1/1 referenceGraphKmers [3]
1259	[153] 0.0 0.00 0.00 1 allocateKmerOccurences [153]
1260	0.00 0.00 1/4665 callocOrExit3 [63]
1261	-----------------------------------------------
1262	0.00 0.00 1/1 newPreGraph_pg [8]
1263	[154] 0.0 0.00 0.00 1 allocatePreNodeSpace_pg [154]
1264	0.00 0.00 1/4665 callocOrExit3 [63]
1265	-----------------------------------------------
1266	0.00 0.00 1/1 exploitShortReadPairs [176]
1267	[155] 0.0 0.00 0.00 1 buildScaffold [155]
1268	0.00 0.00 4006/6010 sequenceCount [55]
1269	0.00 0.00 3862/10691 getShortReadMarkerAtIndex [41]
1270	0.00 0.00 3862/14519 getShortReadMarkerID [34]
1271	0.00 0.00 3566/352440 getNodeInGraph [20]
1272	0.00 0.00 2376/4137 getMarker [65]
1273	0.00 0.00 1931/3845 getShortReadMarkerPosition [68]
1274	0.00 0.00 1931/3845 getShortReadMarkerOffset [67]
1275	0.00 0.00 1193/17234 nodeCount [32]
1276	0.00 0.00 1188/3239 getNodeReads [74]
1277	0.00 0.00 1188/3239 getNodeReadCount [73]
1278	0.00 0.00 595/595 projectFromNode [99]
1279	0.00 0.00 10/4665 callocOrExit3 [63]
1280	0.00 0.00 7/113 velvetLog [128]
1281	0.00 0.00 1/4295 getWordLength [64]
1282	0.00 0.00 1/2 getSequenceLengths [145]
1283	0.00 0.00 1/310 destroyRecycleBin [113]
1284	0.00 0.00 1/1 removeUnreliableConnections [198]
1285	-----------------------------------------------
1286	0.00 0.00 1/1 exploitShortReadPairs [176]
1287	[156] 0.0 0.00 0.00 1 cleanScaffoldMemory [156]
1288	0.00 0.00 1/310 destroyRecycleBin [113]
1289	-----------------------------------------------
1290	0.00 0.00 1/1 main [1]
1291	[157] 0.0 0.00 0.00 1 clipTips_pg [157]
1292	0.00 0.00 1190/1190 isEligibleTip [87]
1293	0.00 0.00 601/9287 preNodeCount_pg [47]
1294	0.00 0.00 598/4088 getPreNodeInPreGraph_pg [66]
1295	0.00 0.00 4/113 velvetLog [128]
1296	0.00 0.00 2/2896 destroyPreNode_pg [78]
1297	0.00 0.00 1/445 getWordLength_pg [109]
1298	0.00 0.00 1/2 concatenatePreGraph_pg [140]
1299	-----------------------------------------------
1300	0.00 0.00 1/1 main [1]
1301	[158] 0.0 0.00 0.00 1 convertSequences [158]
1302	0.00 0.00 1/1 newTightStringArrayFromStringArray [188]
1303	-----------------------------------------------
1304	0.00 0.00 1/1 main [1]
1305	[159] 0.0 0.00 0.00 1 correctGraph [159]
1306	0.00 0.00 2983/17234 nodeCount [32]
1307	0.00 0.00 1788/8272 getNodeID [49]
1308	0.00 0.00 1784/352440 getNodeInGraph [20]
1309	0.00 0.00 1485/5645 getArc [60]
1310	0.00 0.00 892/1118 fh_extractmin [92]
1311	0.00 0.00 892/1118 removeNextNodeFromHeap [93]
1312	0.00 0.00 596/156159 getNodeStatus [22]
1313	0.00 0.00 594/891 fh_insertkey [94]
1314	0.00 0.00 594/891 insertNodeIntoHeap [95]
1315	0.00 0.00 298/299 newFibHeap [118]
1316	0.00 0.00 298/299 fh_deleteheap [116]
1317	0.00 0.00 298/299 destroyHeap [115]
1318	0.00 0.00 298/9792 setSingleNodeStatus [46]
1319	0.00 0.00 298/888 dfh_extractmin [96]
1320	0.00 0.00 298/888 removeNextNodeFromDHeap [97]
1321	0.00 0.00 297/297 setNodeStatus [122]
1322	0.00 0.00 7/113 velvetLog [128]
1323	0.00 0.00 5/3173 mallocOrExit3 [75]
1324	0.00 0.00 5/4665 callocOrExit3 [63]
1325	0.00 0.00 3/3 getMultiplicity [137]
1326	0.00 0.00 3/6 getNextArc [133]
1327	0.00 0.00 3/1209 getDestination [86]
1328	0.00 0.00 2/291 newTightString [125]
1329	0.00 0.00 2/291 destroyTightString [124]
1330	0.00 0.00 1/4295 getWordLength [64]
1331	0.00 0.00 1/2 newDFibHeap [146]
1332	0.00 0.00 1/4 resetNodeStatus [135]
1333	0.00 0.00 1/5940 allocatePointer [56]
1334	0.00 0.00 1/1 activateArcLookupTable [149]
1335	0.00 0.00 1/1 deactivateArcLookupTable [162]
1336	0.00 0.00 1/7 concatenateGraph [132]
1337	0.00 0.00 1/2 clipTipsHard [139]
1338	0.00 0.00 1/2 dfh_deleteheap [142]
1339	0.00 0.00 1/2 destroyDHeap [141]
1340	0.00 0.00 1/310 destroyRecycleBin [113]
1341	0.00 0.00 1/308 newRecycleBin [114]
1342	0.00 0.00 1/1 getArcBetweenNodes [179]
1343	0.00 0.00 1/118903 getNodeLength [25]
1344	0.00 0.00 1/5869 deallocatePointer [57]
1345	0.00 0.00 1/1 dfh_insertkey [173]
1346	0.00 0.00 1/1 insertNodeIntoDHeap [182]
1347	-----------------------------------------------
1348	0.00 0.00 1/1 concatenatePreNodes [110]
1349	[160] 0.0 0.00 0.00 1 createAnalogousPreArc_pg [160]
1350	0.00 0.00 1/2896 allocArrayAllocate [77]
1351	-----------------------------------------------
1352	0.00 0.00 1/1 main [1]
1353	[161] 0.0 0.00 0.00 1 createReadPairingArray [161]
1354	0.00 0.00 1/3173 mallocOrExit3 [75]
1355	-----------------------------------------------
1356	0.00 0.00 1/1 correctGraph [159]
1357	[162] 0.0 0.00 0.00 1 deactivateArcLookupTable [162]
1358	-----------------------------------------------
1359	0.00 0.00 1/1 exploitShortReadPairs [176]
1360	[163] 0.0 0.00 0.00 1 deactivateLocalCorrectionSettings [163]
1361	0.00 0.00 2/291 destroyTightString [124]
1362	0.00 0.00 1/113 velvetLog [128]
1363	0.00 0.00 1/2 dfh_deleteheap [142]
1364	0.00 0.00 1/2 destroyDHeap [141]
1365	-----------------------------------------------
1366	0.00 0.00 1/1 destroyGraph [167]
1367	[164] 0.0 0.00 0.00 1 destroyAllPassageMarkers [164]
1368	-----------------------------------------------
1369	0.00 0.00 1/1 destroyPreGraph_pg [169]
1370	[165] 0.0 0.00 0.00 1 destroyAllocArray [165]
1371	-----------------------------------------------
1372	0.00 0.00 1/1 destroyNode [119]
1373	[166] 0.0 0.00 0.00 1 destroyArc [166]
1374	-----------------------------------------------
1375	0.00 0.00 1/1 main [1]
1376	[167] 0.0 0.00 0.00 1 destroyGraph [167]
1377	0.00 0.00 297/5869 deallocatePointer [57]
1378	0.00 0.00 297/297 destroyNode [119]
1379	0.00 0.00 3/310 destroyRecycleBin [113]
1380	0.00 0.00 1/1 destroyAllPassageMarkers [164]
1381	-----------------------------------------------
1382	0.00 0.00 1/1 importPreGraph [2]
1383	[168] 0.0 0.00 0.00 1 destroyKmerOccurenceTable [168]
1384	-----------------------------------------------
1385	0.00 0.00 1/1 main [1]
1386	[169] 0.0 0.00 0.00 1 destroyPreGraph_pg [169]
1387	0.00 0.00 1/1 destroyAllocArray [165]
1388	-----------------------------------------------
1389	0.00 0.00 1/1 main [1]
1390	[170] 0.0 0.00 0.00 1 destroyReadSet [170]
1391	-----------------------------------------------
1392	0.00 0.00 1/1 newPreGraph_pg [8]
1393	[171] 0.0 0.00 0.00 1 destroyRoadMapArray [171]
1394	-----------------------------------------------
1395	0.00 0.00 1/1 main [1]
1396	[172] 0.0 0.00 0.00 1 detachDubiousReads [172]
1397	-----------------------------------------------
1398	0.00 0.00 1/1 correctGraph [159]
1399	[173] 0.0 0.00 0.00 1 dfh_insertkey [173]
1400	0.00 0.00 1/5940 allocatePointer [56]
1401	-----------------------------------------------
1402	0.00 0.00 1/1 main [1]
1403	[174] 0.0 0.00 0.00 1 displayGeneralStatistics [174]
1404	0.00 0.00 2979/421263 velvetFprintf [16]
1405	0.00 0.00 2079/118903 getNodeLength [25]
1406	0.00 0.00 1090/10691 getShortReadMarkerAtIndex [41]
1407	0.00 0.00 1090/14519 getShortReadMarkerID [34]
1408	0.00 0.00 594/1184 arcCount [89]
1409	0.00 0.00 594/594 getVirtualCoverage [101]
1410	0.00 0.00 594/594 getOriginalVirtualCoverage [100]
1411	0.00 0.00 298/17234 nodeCount [32]
1412	0.00 0.00 297/352440 getNodeInGraph [20]
1413	0.00 0.00 297/7103 getTwinNode [52]
1414	0.00 0.00 297/8272 getNodeID [49]
1415	0.00 0.00 297/584 readCoverage [107]
1416	0.00 0.00 297/297 markerCount [121]
1417	0.00 0.00 297/588 readStartsAreActivated [106]
1418	0.00 0.00 297/3239 getNodeReadCount [73]
1419	0.00 0.00 297/3239 getNodeReads [74]
1420	0.00 0.00 1/113 velvetLog [128]
1421	-----------------------------------------------
1422	0.00 0.00 1/1 newPreGraph_pg [8]
1423	[175] 0.0 0.00 0.00 1 emptyPreGraph_pg [175]
1424	0.00 0.00 1/3173 mallocOrExit3 [75]
1425	-----------------------------------------------
1426	0.00 0.00 1/1 main [1]
1427	[176] 0.0 0.00 0.00 1 exploitShortReadPairs [176]
1428	0.00 0.00 590/590 expandLongNode [103]
1429	0.00 0.00 299/17234 nodeCount [32]
1430	0.00 0.00 297/352440 getNodeInGraph [20]
1431	0.00 0.00 297/2966 getUniqueness [76]
1432	0.00 0.00 295/7103 getTwinNode [52]
1433	0.00 0.00 2/113 velvetLog [128]
1434	0.00 0.00 1/588 readStartsAreActivated [106]
1435	0.00 0.00 1/4 resetNodeStatus [135]
1436	0.00 0.00 1/1 buildScaffold [155]
1437	0.00 0.00 1/1 prepareGraphForLocalCorrections [191]
1438	0.00 0.00 1/4665 callocOrExit3 [63]
1439	0.00 0.00 1/1 cleanScaffoldMemory [156]
1440	0.00 0.00 1/310 destroyRecycleBin [113]
1441	0.00 0.00 1/1 deactivateLocalCorrectionSettings [163]
1442	0.00 0.00 1/8 sortGapMarkers [131]
1443	-----------------------------------------------
1444	0.00 0.00 1/1 main [1]
1445	[177] 0.0 0.00 0.00 1 exportLongNodeSequences [177]
1446	0.00 0.00 298/17234 nodeCount [32]
1447	0.00 0.00 297/352440 getNodeInGraph [20]
1448	0.00 0.00 297/118903 getNodeLength [25]
1449	0.00 0.00 287/291 destroyTightString [124]
1450	0.00 0.00 287/287 exportLongNodeSequence [127]
1451	0.00 0.00 1/113 velvetLog [128]
1452	-----------------------------------------------
1453	0.00 0.00 1/1 main [1]
1454	[178] 0.0 0.00 0.00 1 exportPreGraph_pg [178]
1455	0.00 0.00 71829/421263 velvetFprintf [16]
1456	0.00 0.00 1/113 velvetLog [128]
1457	-----------------------------------------------
1458	0.00 0.00 1/1 correctGraph [159]
1459	[179] 0.0 0.00 0.00 1 getArcBetweenNodes [179]
1460	-----------------------------------------------
1461	0.00 0.00 1/1 main [1]
1462	[180] 0.0 0.00 0.00 1 importReadSet [180]
1463	0.00 0.00 2000/3173 mallocOrExit3 [75]
1464	0.00 0.00 4/4665 callocOrExit3 [63]
1465	0.00 0.00 3/113 velvetLog [128]
1466	-----------------------------------------------
1467	0.00 0.00 1/1 main [1]
1468	[181] 0.0 0.00 0.00 1 importRoadMapArray [181]
1469	0.00 0.00 3/4665 callocOrExit3 [63]
1470	0.00 0.00 2/3173 mallocOrExit3 [75]
1471	0.00 0.00 2/113 velvetLog [128]
1472	0.00 0.00 1/2 resetWordFilter [148]
1473	-----------------------------------------------
1474	0.00 0.00 1/1 correctGraph [159]
1475	[182] 0.0 0.00 0.00 1 insertNodeIntoDHeap [182]
1476	-----------------------------------------------
1477	0.00 0.00 1/1 main [1]
1478	[183] 0.0 0.00 0.00 1 logFinalStats [183]
1479	0.00 0.00 601/118903 getNodeLength [25]
1480	0.00 0.00 597/17234 nodeCount [32]
1481	0.00 0.00 594/352440 getNodeInGraph [20]
1482	0.00 0.00 2/3173 mallocOrExit3 [75]
1483	0.00 0.00 2/421263 velvetFprintf [16]
1484	0.00 0.00 1/6010 sequenceCount [55]
1485	0.00 0.00 1/1 usedReads [201]
1486	0.00 0.00 1/1 n50 [185]
1487	-----------------------------------------------
1488	0.00 0.00 1/1 main [1]
1489	[184] 0.0 0.00 0.00 1 logInstructions [184]
1490	0.00 0.00 8/421263 velvetFprintf [16]
1491	0.00 0.00 1/3173 mallocOrExit3 [75]
1492	-----------------------------------------------
1493	0.00 0.00 1/1 logFinalStats [183]
1494	[185] 0.0 0.00 0.00 1 n50 [185]
1495	0.00 0.00 820/118903 getNodeLength [25]
1496	0.00 0.00 299/17234 nodeCount [32]
1497	0.00 0.00 297/352440 getNodeInGraph [20]
1498	0.00 0.00 297/891 fh_insertkey [94]
1499	0.00 0.00 297/891 insertNodeIntoHeap [95]
1500	0.00 0.00 226/1118 fh_extractmin [92]
1501	0.00 0.00 226/1118 removeNextNodeFromHeap [93]
1502	0.00 0.00 1/299 newFibHeap [118]
1503	0.00 0.00 1/299 fh_deleteheap [116]
1504	0.00 0.00 1/299 destroyHeap [115]
1505	-----------------------------------------------
1506	0.00 0.00 1/1 createPreArc_pg [54]
1507	[186] 0.0 0.00 0.00 1 newAllocArray [186]
1508	0.00 0.00 3/3173 mallocOrExit3 [75]
1509	-----------------------------------------------
1510	0.00 0.00 1/1 referenceGraphKmers [3]
1511	[187] 0.0 0.00 0.00 1 newKmerOccurenceTable [187]
1512	0.00 0.00 1/3173 mallocOrExit3 [75]
1513	0.00 0.00 1/1 resetKeyFilter [199]
1514	0.00 0.00 1/4665 callocOrExit3 [63]
1515	-----------------------------------------------
1516	0.00 0.00 1/1 convertSequences [158]
1517	[188] 0.0 0.00 0.00 1 newTightStringArrayFromStringArray [188]
1518	0.00 0.00 1/3173 mallocOrExit3 [75]
1519	0.00 0.00 1/4665 callocOrExit3 [63]
1520	-----------------------------------------------
1521	0.00 0.00 1/1 importPreGraph [2]
1522	[189] 0.0 0.00 0.00 1 orderNodeReadStartArrays [189]
1523	-----------------------------------------------
1524	0.00 0.00 1/1 main [1]
1525	[190] 0.0 0.00 0.00 1 pairedCategories [190]
1526	-----------------------------------------------
1527	0.00 0.00 1/1 exploitShortReadPairs [176]
1528	[191] 0.0 0.00 0.00 1 prepareGraphForLocalCorrections [191]
1529	0.00 0.00 597/17234 nodeCount [32]
1530	0.00 0.00 102/4665 callocOrExit3 [63]
1531	0.00 0.00 3/3173 mallocOrExit3 [75]
1532	0.00 0.00 2/291 newTightString [125]
1533	0.00 0.00 1/4295 getWordLength [64]
1534	0.00 0.00 1/113 velvetLog [128]
1535	0.00 0.00 1/2 newDFibHeap [146]
1536	-----------------------------------------------
1537	0.00 0.00 1/1 main [1]
1538	[192] 0.0 0.00 0.00 1 readCoherentGraph [192]
1539	0.00 0.00 897/17234 nodeCount [32]
1540	0.00 0.00 891/352440 getNodeInGraph [20]
1541	0.00 0.00 891/2966 getUniqueness [76]
1542	0.00 0.00 590/590 uniqueNodesConnect [105]
1543	0.00 0.00 297/297 isUniqueSolexa [120]
1544	0.00 0.00 297/297 setUniqueness [123]
1545	0.00 0.00 295/7103 getTwinNode [52]
1546	0.00 0.00 5/113 velvetLog [128]
1547	0.00 0.00 2/4137 getMarker [65]
1548	0.00 0.00 1/308 newRecycleBin [114]
1549	0.00 0.00 1/4 resetNodeStatus [135]
1550	0.00 0.00 1/8 renumberNodes [130]
1551	0.00 0.00 1/310 destroyRecycleBin [113]
1552	-----------------------------------------------
1553	0.00 0.00 1/1 importPreGraph [2]
1554	[193] 0.0 0.00 0.00 1 readPreGraphFile [193]
1555	0.00 0.00 595/4665 callocOrExit3 [63]
1556	0.00 0.00 594/5940 allocatePointer [56]
1557	0.00 0.00 2/113 velvetLog [128]
1558	0.00 0.00 1/3173 mallocOrExit3 [75]
1559	0.00 0.00 1/2 resetWordFilter [148]
1560	0.00 0.00 1/308 newRecycleBin [114]
1561	-----------------------------------------------
1562	0.00 0.00 1/1 main [1]
1563	[194] 0.0 0.00 0.00 1 removeHighCoverageNodes [194]
1564	-----------------------------------------------
1565	0.00 0.00 1/1 main [1]
1566	[195] 0.0 0.00 0.00 1 removeLowCoverageNodesAndDenounceDubiousReads [195]
1567	0.00 0.00 1188/118903 getNodeLength [25]
1568	0.00 0.00 596/17234 nodeCount [32]
1569	0.00 0.00 594/352440 getNodeInGraph [20]
1570	0.00 0.00 594/1475 getTotalCoverage [84]
1571	0.00 0.00 3/113 velvetLog [128]
1572	0.00 0.00 2/7 concatenateGraph [132]
1573	0.00 0.00 1/588 readStartsAreActivated [106]
1574	0.00 0.00 1/6010 sequenceCount [55]
1575	0.00 0.00 1/4665 callocOrExit3 [63]
1576	-----------------------------------------------
1577	0.00 0.00 1/1 main [1]
1578	[196] 0.0 0.00 0.00 1 removeLowCoverageReferenceNodes [196]
1579	0.00 0.00 891/118903 getNodeLength [25]
1580	0.00 0.00 298/17234 nodeCount [32]
1581	0.00 0.00 297/352440 getNodeInGraph [20]
1582	0.00 0.00 297/1475 getTotalCoverage [84]
1583	0.00 0.00 297/4137 getMarker [65]
1584	0.00 0.00 1/113 velvetLog [128]
1585	-----------------------------------------------
1586	0.00 0.00 1/1 main [1]
1587	[197] 0.0 0.00 0.00 1 removeLowLongCoverageNodesAndDenounceDubiousReads [197]
1588	0.00 0.00 1/588 readStartsAreActivated [106]
1589	-----------------------------------------------
1590	0.00 0.00 1/1 buildScaffold [155]
1591	[198] 0.0 0.00 0.00 1 removeUnreliableConnections [198]
1592	0.00 0.00 1914/10691 getShortReadMarkerAtIndex [41]
1593	0.00 0.00 1914/14519 getShortReadMarkerID [34]
1594	0.00 0.00 595/352440 getNodeInGraph [20]
1595	0.00 0.00 594/2966 getUniqueness [76]
1596	0.00 0.00 590/3239 getNodeReads [74]
1597	0.00 0.00 590/3239 getNodeReadCount [73]
1598	0.00 0.00 3/17234 nodeCount [32]
1599	0.00 0.00 3/3 getInsertLength [136]
1600	0.00 0.00 1/4665 callocOrExit3 [63]
1601	-----------------------------------------------
1602	0.00 0.00 1/1 newKmerOccurenceTable [187]
1603	[199] 0.0 0.00 0.00 1 resetKeyFilter [199]
1604	-----------------------------------------------
1605	0.00 0.00 1/1 main [1]
1606	[200] 0.0 0.00 0.00 1 setProgramName [200]
1607	-----------------------------------------------
1608	0.00 0.00 1/1 logFinalStats [183]
1609	[201] 0.0 0.00 0.00 1 usedReads [201]
1610	0.00 0.00 2002/6010 sequenceCount [55]
1611	0.00 0.00 1911/10691 getShortReadMarkerAtIndex [41]
1612	0.00 0.00 1911/14519 getShortReadMarkerID [34]
1613	0.00 0.00 574/3239 getNodeReads [74]
1614	0.00 0.00 574/3239 getNodeReadCount [73]
1615	0.00 0.00 574/7103 getTwinNode [52]
1616	0.00 0.00 298/17234 nodeCount [32]
1617	0.00 0.00 297/352440 getNodeInGraph [20]
1618	0.00 0.00 297/118903 getNodeLength [25]
1619	0.00 0.00 287/4137 getMarker [65]
1620	0.00 0.00 287/588 readStartsAreActivated [106]
1621	0.00 0.00 1/4665 callocOrExit3 [63]
1622	-----------------------------------------------
1623
1624	This table describes the call tree of the program, and was sorted by
1625	the total amount of time spent in each function and its children.
1626
1627	Each entry in this table consists of several lines. The line with the
1628	index number at the left hand margin lists the current function.
1629	The lines above it list the functions that called this function,
1630	and the lines below it list the functions this one called.
1631	This line lists:
1632	index A unique number given to each element of the table.
1633	Index numbers are sorted numerically.
1634	The index number is printed next to every function name so
1635	it is easier to look up where the function in the table.
1636
1637	% time This is the percentage of the `total' time that was spent
1638	in this function and its children. Note that due to
1639	different viewpoints, functions excluded by options, etc,
1640	these numbers will NOT add up to 100%.
1641
1642	self This is the total amount of time spent in this function.
1643
1644	children This is the total amount of time propagated into this
1645	function by its children.
1646
1647	called This is the number of times the function was called.
1648	If the function called itself recursively, the number
1649	only includes non-recursive calls, and is followed by
1650	a `+' and the number of recursive calls.
1651
1652	name The name of the current function. The index number is
1653	printed after it. If the function is a member of a
1654	cycle, the cycle number is printed between the
1655	function's name and the index number.
1656
1657
1658	For the function's parents, the fields have the following meanings:
1659
1660	self This is the amount of time that was propagated directly
1661	from the function into this parent.
1662
1663	children This is the amount of time that was propagated from
1664	the function's children into this parent.
1665
1666	called This is the number of times this parent called the
1667	function `/' the total number of times the function
1668	was called. Recursive calls to the function are not
1669	included in the number after the `/'.
1670
1671	name This is the name of the parent. The parent's index
1672	number is printed after it. If the parent is a
1673	member of a cycle, the cycle number is printed between
1674	the name and the index number.
1675
1676	If the parents of the function cannot be determined, the word
1677	`<spontaneous>' is printed in the `name' field, and all the other
1678	fields are blank.
1679
1680	For the function's children, the fields have the following meanings:
1681
1682	self This is the amount of time that was propagated directly
1683	from the child into the function.
1684
1685	children This is the amount of time that was propagated from the
1686	child's children to the function.
1687
1688	called This is the number of times the function called
1689	this child `/' the total number of times the child
1690	was called. Recursive calls by the child are not
1691	listed in the number after the `/'.
1692
1693	name This is the name of the child. The child's index
1694	number is printed after it. If the child is a
1695	member of a cycle, the cycle number is printed
1696	between the name and the index number.
1697
1698	If there are any cycles (circles) in the call graph, there is an
1699	entry for the cycle-as-a-whole. This entry shows who called the
1700	cycle (as parents) and the members of the cycle (as children.)
1701	The `+' recursive calls entry shows the number of function calls that
1702	were internal to the cycle, and the calls entry for each member shows,
1703	for that member, how many times it was called from other members of
1704	the cycle.
1705
1706
1707	Index by function name
1708
1709	[149] activateArcLookupTable [94] fh_insertkey [71] isLoop_pg
1710	[150] activateGapMarkers [117] fh_makekeyheap [120] isUniqueSolexa
1711	[151] activateReadStarts [5] findKmerInKmerOccurenceTable [183] logFinalStats
1712	[9] addPreNodeToPreGraph_pg [35] getAnnotSequenceID [184] logInstructions
1713	[81] addReadStart [44] getAnnotationCount [75] mallocOrExit3
1714	[77] allocArrayAllocate [26] getAnnotationLength [121] markerCount
1715	[79] allocArrayFree [60] getArc [185] n50
1716	[152] allocateArc [179] getArcBetweenNodes [186] newAllocArray
1717	[153] allocateKmerOccurences [90] getConnection [146] newDFibHeap
1718	[56] allocatePointer [86] getDestination [118] newFibHeap
1719	[154] allocatePreNodeSpace_pg [38] getDestination_pg [187] newKmerOccurenceTable
1720	[72] appendDescriptors_pg [30] getFinish [8] newPreGraph_pg
1721	[89] arcCount [53] getFinishID [114] newRecycleBin
1722	[155] buildScaffold [108] getGap [125] newTightString
1723	[63] callocOrExit3 [136] getInsertLength [188] newTightStringArrayFromStringArray
1724	[156] cleanScaffoldMemory [42] getInsertionMarkerPosition [32] nodeCount
1725	[43] clearKmer [18] getKmerKey [189] orderNodeReadStartArrays
1726	[139] clipTipsHard [21] getKmerOccurenceNodeID [190] pairedCategories
1727	[157] clipTips_pg [23] getKmerOccurencePosition [29] popNucleotide
1728	[6] compareKmers [17] getLength [47] preNodeCount_pg
1729	[132] concatenateGraph [91] getMarkedNodeList [191] prepareGraphForLocalCorrections
1730	[140] concatenatePreGraph_pg [65] getMarker [99] projectFromNode
1731	[110] concatenatePreNodes [137] getMultiplicity [134] projectFromSingleRead
1732	[158] convertSequences [39] getNextAnnotation [104] pushNeighbours
1733	[11] copyKmers [133] getNextArc [14] pushNucleotide
1734	[159] correctGraph [58] getNextPreArc_pg [192] readCoherentGraph
1735	[102] correctGraphLocally [49] getNodeID [107] readCoverage
1736	[160] createAnalogousPreArc_pg [20] getNodeInGraph [193] readPreGraphFile
1737	[82] createArc [25] getNodeLength [106] readStartsAreActivated
1738	[12] createNodeReadStartArrays [73] getNodeReadCount [129] reallocOrExit4
1739	[54] createPreArc_pg [74] getNodeReads [13] recordKmerOccurence
1740	[7] createPreNodes [22] getNodeStatus [3] referenceGraphKmers
1741	[161] createReadPairingArray [19] getNucleotide [111] referenceMarkersAreActivated_pg
1742	[162] deactivateArcLookupTable [27] getNucleotideChar [194] removeHighCoverageNodes
1743	[163] deactivateLocalCorrectionSettings [100] getOriginalVirtualCoverage [195] removeLowCoverageNodesAndDenounceDubiousReads
1744	[57] deallocatePointer [70] getOtherEnd_pg [196] removeLowCoverageReferenceNodes
1745	[164] destroyAllPassageMarkers [36] getPosition [197] removeLowLongCoverageNodesAndDenounceDubiousReads
1746	[165] destroyAllocArray [37] getPreArc_pg [97] removeNextNodeFromDHeap
1747	[166] destroyArc [66] getPreNodeInPreGraph_pg [93] removeNextNodeFromHeap
1748	[141] destroyDHeap [33] getPreNodeLength_pg [59] removePreArcFromList_pg
1749	[167] destroyGraph [45] getRoadMapInArray [198] removeUnreliableConnections
1750	[115] destroyHeap [145] getSequenceLengths [130] renumberNodes
1751	[168] destroyKmerOccurenceTable [41] getShortReadMarkerAtIndex [147] renumberPreNodes_pg
1752	[119] destroyNode [34] getShortReadMarkerID [199] resetKeyFilter
1753	[169] destroyPreGraph_pg [67] getShortReadMarkerOffset [135] resetNodeStatus
1754	[78] destroyPreNode_pg [68] getShortReadMarkerPosition [148] resetWordFilter
1755	[170] destroyReadSet [31] getStart [15] reversePushNucleotide
1756	[113] destroyRecycleBin [61] getStartID [55] sequenceCount
1757	[171] destroyRoadMapArray [50] getTightStringInArray [40] sequenceCount_pg
1758	[124] destroyTightString [88] getTipLength [69] setFinishID
1759	[172] detachDubiousReads [84] getTotalCoverage [138] setInsertLengths
1760	[142] dfh_deleteheap [52] getTwinNode [122] setNodeStatus
1761	[96] dfh_extractmin [76] getUniqueness [112] setPreNodeDescriptor_pg
1762	[173] dfh_insertkey [101] getVirtualCoverage [200] setProgramName
1763	[143] dfh_makekeyheap [64] getWordLength [46] setSingleNodeStatus
1764	[174] displayGeneralStatistics [109] getWordLength_pg [62] setStartID
1765	[175] emptyPreGraph_pg [48] hasSinglePreArc_pg [123] setUniqueness
1766	[103] expandLongNode [2] importPreGraph [51] simpleArcCount
1767	[126] expandNode [180] importReadSet [80] simplePreArcCount_pg
1768	[176] exploitShortReadPairs [181] importRoadMapArray [131] sortGapMarkers
1769	[144] exportGraph [85] incrementAnnotationCoordinates [4] sortKmerOccurenceTable
1770	[127] exportLongNodeSequence [24] incrementOriginalVirtualCoverage [105] uniqueNodesConnect
1771	[177] exportLongNodeSequences [83] incrementReadStartCount [201] usedReads
1772	[178] exportPreGraph_pg [10] incrementVirtualCoverage [16] velvetFprintf
1773	[98] fh_consolidate [182] insertNodeIntoDHeap [128] velvetLog
1774	[116] fh_deleteheap [95] insertNodeIntoHeap [28] writeNucleotideAtPosition
1775	[92] fh_extractmin [87] isEligibleTip

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