finishm 0.0.1
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- data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
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- data/spec/explore_spec.rb +29 -0
- data/spec/fluffer_spec.rb +155 -0
- data/spec/gapfiller_spec.rb +107 -0
- data/spec/graph_explorer_spec.rb +475 -0
- data/spec/graph_generator_spec.rb +99 -0
- data/spec/height_finder_spec.rb +306 -0
- data/spec/kmer_abundance_pattern_spec.rb +56 -0
- data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
- data/spec/kmer_profile_finder_spec.rb +38 -0
- data/spec/kmers_count_tabulate_spec.rb +120 -0
- data/spec/oriented_node_trail_spec.rb +221 -0
- data/spec/paired_end_neighbours_spec.rb +126 -0
- data/spec/paths_between_nodes_spec.rb +349 -0
- data/spec/priner_spec.rb +7 -0
- data/spec/read_input_spec.rb +23 -0
- data/spec/read_selection_by_kmer_spec.rb +166 -0
- data/spec/read_to_node_spec.rb +35 -0
- data/spec/roundup_spec.rb +366 -0
- data/spec/scaffold_breaker_spec.rb +144 -0
- data/spec/sequence_spec.rb +43 -0
- data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
- data/spec/single_coherent_wanderer_spec.rb +120 -0
- data/spec/single_ended_assembler_spec.rb +398 -0
- data/spec/spec_helper.rb +310 -0
- data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
- data/spec/visualise_spec.rb +105 -0
- data/spec/wander_spec.rb +119 -0
- data/spec/watch_for_changes.sh +16 -0
- data/validation/fasta_compare.rb +72 -0
- data/validation/gapfill_simulate_perfect.rb +108 -0
- metadata +899 -0
data/ext/src/src/fib.h
ADDED
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/*
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Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
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This file is part of Velvet.
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Velvet is free software; you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation; either version 2 of the License, or
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(at your option) any later version.
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Velvet is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with Velvet; if not, write to the Free Software
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Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
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*/
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/*-
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* Copyright 1997, 1998-2003 John-Mark Gurney.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions
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* are met:
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* 1. Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright
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* notice, this list of conditions and the following disclaimer in the
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* THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
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* ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
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* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
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* OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
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* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
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* OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
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* SUCH DAMAGE.
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* $Id: fib.h,v 1.9 2007/04/24 12:16:41 zerbino Exp $
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#ifndef _FIB_H_
|
51
|
+
#define _FIB_H_
|
52
|
+
|
53
|
+
#include "globals.h"
|
54
|
+
|
55
|
+
typedef Coordinate(*voidcmp) (void *, void *);
|
56
|
+
|
57
|
+
/* functions for key heaps */
|
58
|
+
FibHeap *fh_makekeyheap(void);
|
59
|
+
FibHeapNode *fh_insertkey(FibHeap *, Coordinate, void *);
|
60
|
+
Coordinate fh_minkey(FibHeap *);
|
61
|
+
Coordinate fh_replacekey(FibHeap *, FibHeapNode *, Coordinate);
|
62
|
+
void *fh_replacekeydata(FibHeap *, FibHeapNode *, Coordinate, void *);
|
63
|
+
|
64
|
+
/* functions for void * heaps */
|
65
|
+
FibHeap *fh_makeheap(void);
|
66
|
+
voidcmp fh_setcmp(FibHeap *, voidcmp);
|
67
|
+
void *fh_setneginf(FibHeap *, void *);
|
68
|
+
FibHeapNode *fh_insert(FibHeap *, void *);
|
69
|
+
|
70
|
+
/* shared functions */
|
71
|
+
void *fh_extractmin(FibHeap *);
|
72
|
+
void *fh_min(FibHeap *);
|
73
|
+
void *fh_replacedata(FibHeapNode *, void *);
|
74
|
+
void *fh_delete(FibHeap *, FibHeapNode *);
|
75
|
+
void fh_deleteheap(FibHeap *);
|
76
|
+
FibHeap *fh_union(FibHeap *, FibHeap *);
|
77
|
+
|
78
|
+
#endif /* _FIB_H_ */
|
@@ -0,0 +1,79 @@
|
|
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
|
+
#include <stdlib.h>
|
22
|
+
|
23
|
+
#include "fib.h"
|
24
|
+
#include "utility.h"
|
25
|
+
|
26
|
+
// Constructor
|
27
|
+
// Memory allocated
|
28
|
+
FibHeap *newFibHeap()
|
29
|
+
{
|
30
|
+
FibHeap * heap = fh_makekeyheap();
|
31
|
+
if (heap == NULL)
|
32
|
+
exitErrorf(EXIT_FAILURE, true, "Can't allocate FibHeap");
|
33
|
+
|
34
|
+
return heap;
|
35
|
+
}
|
36
|
+
|
37
|
+
// Add new node into heap with a key, and a pointer to the specified node
|
38
|
+
FibHeapNode *insertNodeIntoHeap(FibHeap * heap, Coordinate key,
|
39
|
+
struct node_st * node)
|
40
|
+
{
|
41
|
+
return fh_insertkey(heap, key, node);
|
42
|
+
}
|
43
|
+
|
44
|
+
// Returns smallest key in heap
|
45
|
+
Coordinate minKeyOfHeap(FibHeap * heap)
|
46
|
+
{
|
47
|
+
return fh_minkey(heap);
|
48
|
+
}
|
49
|
+
|
50
|
+
// Replaces the key for a given node
|
51
|
+
Coordinate replaceKeyInHeap(FibHeap * heap, FibHeapNode * node,
|
52
|
+
Coordinate newKey)
|
53
|
+
{
|
54
|
+
return fh_replacekey(heap, node, newKey);
|
55
|
+
}
|
56
|
+
|
57
|
+
// Removes the node with the shortest key, then returns it.
|
58
|
+
struct node_st *removeNextNodeFromHeap(FibHeap * heap)
|
59
|
+
{
|
60
|
+
return (struct node_st *) fh_extractmin(heap);
|
61
|
+
}
|
62
|
+
|
63
|
+
// Destructor
|
64
|
+
void destroyHeap(FibHeap * heap)
|
65
|
+
{
|
66
|
+
fh_deleteheap(heap);
|
67
|
+
}
|
68
|
+
|
69
|
+
// Replace the node pointed to by a heap node
|
70
|
+
void replaceValueInHeap(FibHeapNode * node, Node * newValue)
|
71
|
+
{
|
72
|
+
fh_replacedata(node, newValue);
|
73
|
+
}
|
74
|
+
|
75
|
+
// Remove unwanted node
|
76
|
+
void destroyNodeInHeap(FibHeapNode * node, FibHeap * heap)
|
77
|
+
{
|
78
|
+
fh_delete(heap, node);
|
79
|
+
}
|
@@ -0,0 +1,41 @@
|
|
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
|
+
#ifndef _FIBHEAP_H_
|
22
|
+
#define _FIBHEAP_H_
|
23
|
+
|
24
|
+
FibHeap *newFibHeap();
|
25
|
+
|
26
|
+
FibHeapNode *insertNodeIntoHeap(FibHeap * heap, Coordinate key,
|
27
|
+
Node * node);
|
28
|
+
|
29
|
+
Coordinate minKeyOfHeap(FibHeap * heap);
|
30
|
+
|
31
|
+
Coordinate replaceKeyInHeap(FibHeap * heap, FibHeapNode * node,
|
32
|
+
Coordinate newKey);
|
33
|
+
|
34
|
+
void replaceValueInHeap(FibHeapNode * node, Node * newValue);
|
35
|
+
|
36
|
+
Node *removeNextNodeFromHeap(FibHeap * heap);
|
37
|
+
|
38
|
+
void *destroyNodeInHeap(FibHeapNode * node, FibHeap * heap);
|
39
|
+
|
40
|
+
void destroyHeap(FibHeap * heap);
|
41
|
+
#endif
|
@@ -0,0 +1,110 @@
|
|
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
|
+
* Copyright 1997, 1999-2003 John-Mark Gurney.
|
23
|
+
* All rights reserved.
|
24
|
+
*
|
25
|
+
* Redistribution and use in source and binary forms, with or without
|
26
|
+
|
27
|
+
* are met:
|
28
|
+
* 1. Redistributions of source code must retain the above copyright
|
29
|
+
* notice, this list of conditions and the following disclaimer.
|
30
|
+
* 2. Redistributions in binary form must reproduce the above copyright
|
31
|
+
* notice, this list of conditions and the following disclaimer in the
|
32
|
+
* documentation and/or other materials provided with the distribution.
|
33
|
+
*
|
34
|
+
* THIS SOFTWARE IS PROVIDED BY THE AUTHOR AND CONTRIBUTORS ``AS IS'' AND
|
35
|
+
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
36
|
+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
37
|
+
* ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR OR CONTRIBUTORS BE LIABLE
|
38
|
+
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
|
39
|
+
* DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
|
40
|
+
* OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
|
41
|
+
* HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
|
42
|
+
* LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
|
43
|
+
* OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
|
44
|
+
* SUCH DAMAGE.
|
45
|
+
*
|
46
|
+
* $Id: fibpriv.h,v 1.10 2007/10/09 09:56:46 zerbino Exp $
|
47
|
+
*
|
48
|
+
*/
|
49
|
+
|
50
|
+
#ifndef _FIBPRIV_H_
|
51
|
+
#define _FIBPRIV_H_
|
52
|
+
|
53
|
+
#include "globals.h"
|
54
|
+
|
55
|
+
/*
|
56
|
+
* specific node operations
|
57
|
+
*/
|
58
|
+
struct fibheap_el {
|
59
|
+
FibHeapNode *fhe_p;
|
60
|
+
FibHeapNode *fhe_child;
|
61
|
+
FibHeapNode *fhe_left;
|
62
|
+
FibHeapNode *fhe_right;
|
63
|
+
void *fhe_data;
|
64
|
+
Coordinate fhe_key;
|
65
|
+
int fhe_degree;
|
66
|
+
boolean fhe_mark;
|
67
|
+
};
|
68
|
+
|
69
|
+
static FibHeapNode *fhe_newelem(struct fibheap *);
|
70
|
+
static void fhe_initelem(FibHeapNode *);
|
71
|
+
static void fhe_insertafter(FibHeapNode * a, FibHeapNode * b);
|
72
|
+
static inline void fhe_insertbefore(FibHeapNode * a, FibHeapNode * b);
|
73
|
+
static FibHeapNode *fhe_remove(FibHeapNode * a);
|
74
|
+
|
75
|
+
/*
|
76
|
+
* global heap operations
|
77
|
+
*/
|
78
|
+
struct fibheap {
|
79
|
+
Coordinate(*fh_cmp_fnct) (void *, void *);
|
80
|
+
RecycleBin *nodeMemory;
|
81
|
+
IDnum fh_n;
|
82
|
+
IDnum fh_Dl;
|
83
|
+
FibHeapNode **fh_cons;
|
84
|
+
FibHeapNode *fh_min;
|
85
|
+
FibHeapNode *fh_root;
|
86
|
+
void *fh_neginf;
|
87
|
+
boolean fh_keys;
|
88
|
+
};
|
89
|
+
|
90
|
+
static void fh_initheap(FibHeap *);
|
91
|
+
static void fh_insertrootlist(FibHeap *, FibHeapNode *);
|
92
|
+
static void fh_removerootlist(FibHeap *, FibHeapNode *);
|
93
|
+
static void fh_consolidate(FibHeap *);
|
94
|
+
static void fh_heaplink(FibHeap * h, FibHeapNode * y, FibHeapNode * x);
|
95
|
+
static void fh_cut(FibHeap *, FibHeapNode *, FibHeapNode *);
|
96
|
+
static void fh_cascading_cut(FibHeap *, FibHeapNode *);
|
97
|
+
static FibHeapNode *fh_extractminel(FibHeap *);
|
98
|
+
static void fh_checkcons(FibHeap * h);
|
99
|
+
static void fh_destroyheap(FibHeap * h);
|
100
|
+
static int fh_compare(FibHeap * h, FibHeapNode * a, FibHeapNode * b);
|
101
|
+
static int fh_comparedata(FibHeap * h, Coordinate key,
|
102
|
+
void *data, FibHeapNode * b);
|
103
|
+
static void fh_insertel(FibHeap * h, FibHeapNode * x);
|
104
|
+
|
105
|
+
/*
|
106
|
+
* general functions
|
107
|
+
*/
|
108
|
+
static inline IDnum ceillog2(IDnum a);
|
109
|
+
|
110
|
+
#endif /* _FIBPRIV_H_ */
|
@@ -0,0 +1,154 @@
|
|
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
|
+
#ifndef _GLOBALS_H_
|
22
|
+
#define _GLOBALS_H_
|
23
|
+
|
24
|
+
#ifndef NULL
|
25
|
+
#define NULL 0
|
26
|
+
#endif
|
27
|
+
|
28
|
+
#ifndef true
|
29
|
+
#define true 1
|
30
|
+
#define false 0
|
31
|
+
#endif
|
32
|
+
|
33
|
+
#ifdef __GNUC__
|
34
|
+
#define ATTRIBUTE_PACKED __attribute__ ((packed))
|
35
|
+
#else
|
36
|
+
#define ATTRIBUTE_PACKED
|
37
|
+
#endif
|
38
|
+
|
39
|
+
#define VERSION_NUMBER 1
|
40
|
+
#define RELEASE_NUMBER 2
|
41
|
+
#define UPDATE_NUMBER 10
|
42
|
+
#define VERSION_BRANCH "-wwood_finishm"
|
43
|
+
|
44
|
+
#define MAXLINE 5000
|
45
|
+
|
46
|
+
#define LONG (2 * CATEGORIES)
|
47
|
+
#define LONG_PAIRED (2 * CATEGORIES + 1)
|
48
|
+
#define REFERENCE (2 * CATEGORIES + 2)
|
49
|
+
|
50
|
+
/* NULL value for ArrayIdx */
|
51
|
+
#define NULL_IDX 0
|
52
|
+
|
53
|
+
#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
|
54
|
+
#define inline __inline
|
55
|
+
extern struct tString_st;
|
56
|
+
extern struct readSet_st;
|
57
|
+
extern struct splayTable_st;
|
58
|
+
extern struct annotation_st;
|
59
|
+
extern struct roadmap_st;
|
60
|
+
extern struct insertionMarker_st;
|
61
|
+
extern struct arc_st;
|
62
|
+
extern struct node_st;
|
63
|
+
extern struct graph_st;
|
64
|
+
extern struct passage_st;
|
65
|
+
extern struct passageList_st;
|
66
|
+
extern struct readStart_st;
|
67
|
+
extern struct preArc_st;
|
68
|
+
extern struct preNode_st;
|
69
|
+
extern struct preGraph_st;
|
70
|
+
extern struct fibheap;
|
71
|
+
extern struct fibheap_el;
|
72
|
+
extern struct dfibheap;
|
73
|
+
extern struct dfibheap_el;
|
74
|
+
extern struct kmerOccurence_st;
|
75
|
+
extern struct kmerOccurenceTable_st;
|
76
|
+
#endif
|
77
|
+
|
78
|
+
// Namespace sizes
|
79
|
+
#include <stdint.h>
|
80
|
+
typedef int8_t boolean;
|
81
|
+
typedef int8_t Nucleotide;
|
82
|
+
typedef uint8_t Descriptor;
|
83
|
+
#ifdef BIGASSEMBLY
|
84
|
+
typedef int64_t IDnum;
|
85
|
+
#else
|
86
|
+
typedef int32_t IDnum;
|
87
|
+
#endif
|
88
|
+
typedef int64_t Coordinate;
|
89
|
+
#ifdef LONGSEQUENCES
|
90
|
+
typedef int32_t ShortLength;
|
91
|
+
#else
|
92
|
+
typedef int16_t ShortLength;
|
93
|
+
#endif
|
94
|
+
typedef double Time;
|
95
|
+
typedef uint8_t Quality;
|
96
|
+
typedef double Probability;
|
97
|
+
typedef int8_t Category;
|
98
|
+
#ifndef VBIGASSEMBLY
|
99
|
+
typedef uint32_t ArrayIdx;
|
100
|
+
#else
|
101
|
+
typedef uint64_t ArrayIdx;
|
102
|
+
#endif
|
103
|
+
|
104
|
+
// Atomic word
|
105
|
+
typedef struct kmer_st Kmer;
|
106
|
+
typedef uint64_t KmerKey;
|
107
|
+
|
108
|
+
// Just a sequence string, but with just two bits per character
|
109
|
+
typedef struct tString_st TightString;
|
110
|
+
|
111
|
+
// A simple container when reading files
|
112
|
+
typedef struct readSet_st ReadSet;
|
113
|
+
typedef struct sequenceReader_st SequenceReader;
|
114
|
+
typedef struct sequencesReader_st SequencesReader;
|
115
|
+
|
116
|
+
// Hash table structures
|
117
|
+
typedef struct kmerOccurence_st KmerOccurence;
|
118
|
+
typedef struct kmerOccurenceTable_st KmerOccurenceTable;
|
119
|
+
typedef struct splayTable_st SplayTable;
|
120
|
+
|
121
|
+
// Graph construction structures
|
122
|
+
typedef struct annotationList_st AnnotationList;
|
123
|
+
typedef struct annotation_st Annotation;
|
124
|
+
typedef struct roadmap_st RoadMap;
|
125
|
+
typedef struct roadMapArray_st RoadMapArray;
|
126
|
+
typedef struct insertionMarker_st InsertionMarker;
|
127
|
+
|
128
|
+
// Pre-Graph elements
|
129
|
+
typedef struct preMarker_st PreMarker;
|
130
|
+
typedef ArrayIdx PreArcI;
|
131
|
+
typedef struct preNode_st PreNode;
|
132
|
+
typedef struct preGraph_st PreGraph;
|
133
|
+
|
134
|
+
// Graph elements
|
135
|
+
typedef struct arc_st Arc;
|
136
|
+
typedef struct node_st Node;
|
137
|
+
typedef struct graph_st Graph;
|
138
|
+
typedef struct shortReadMarker_st ShortReadMarker;
|
139
|
+
typedef ArrayIdx PassageMarkerI;
|
140
|
+
typedef struct passageList_st PassageMarkerList;
|
141
|
+
typedef struct readStart_st ReadStart;
|
142
|
+
typedef struct gapMarker_st GapMarker;
|
143
|
+
|
144
|
+
// Fibonacci heaps used mainly in Tour Bus
|
145
|
+
typedef struct fibheap FibHeap;
|
146
|
+
typedef struct fibheap_el FibHeapNode;
|
147
|
+
typedef struct dfibheap DFibHeap;
|
148
|
+
typedef struct dfibheap_el DFibHeapNode;
|
149
|
+
|
150
|
+
typedef struct nodeList_st NodeList;
|
151
|
+
|
152
|
+
typedef struct mask_st Mask;
|
153
|
+
|
154
|
+
#endif
|