finishm 0.0.1
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- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
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- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
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- data/lib/assembly/a_b_visualiser.rb +169 -0
- data/lib/assembly/acyclic_connection_finder.rb +81 -0
- data/lib/assembly/all_orfs.rb +615 -0
- data/lib/assembly/bad_format_writer.rb +46 -0
- data/lib/assembly/bam_probe_read_selector.rb +48 -0
- data/lib/assembly/bubbly_assembler.rb +842 -0
- data/lib/assembly/c_probe_node_finder.rb +38 -0
- data/lib/assembly/connection_interpreter.rb +350 -0
- data/lib/assembly/contig_printer.rb +400 -0
- data/lib/assembly/coverage_based_graph_filter.rb +68 -0
- data/lib/assembly/depth_first_search.rb +63 -0
- data/lib/assembly/dijkstra.rb +216 -0
- data/lib/assembly/fluffer.rb +253 -0
- data/lib/assembly/graph_explorer.rb +85 -0
- data/lib/assembly/graph_generator.rb +315 -0
- data/lib/assembly/height_finder.rb +355 -0
- data/lib/assembly/hybrid_velvet_graph.rb +70 -0
- data/lib/assembly/input_genome.rb +182 -0
- data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
- data/lib/assembly/node_finder.rb +171 -0
- data/lib/assembly/oriented_node_trail.rb +507 -0
- data/lib/assembly/paired_end_assembler.rb +53 -0
- data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
- data/lib/assembly/probed_graph.rb +105 -0
- data/lib/assembly/read_input.rb +79 -0
- data/lib/assembly/read_to_node.rb +37 -0
- data/lib/assembly/scaffold_breaker.rb +126 -0
- data/lib/assembly/sequence_hasher.rb +71 -0
- data/lib/assembly/single_coherent_paths_between_nodes.rb +533 -0
- data/lib/assembly/single_coherent_wanderer.rb +261 -0
- data/lib/assembly/single_ended_assembler.rb +441 -0
- data/lib/assembly/velvet_c_binding.rb +54 -0
- data/lib/assembly/velvet_graph_sequence_extractor.rb +123 -0
- data/lib/external/VERSION +1 -0
- data/lib/finishm/assemble.rb +224 -0
- data/lib/finishm/explore.rb +217 -0
- data/lib/finishm/finisher.rb +303 -0
- data/lib/finishm/fluff.rb +122 -0
- data/lib/finishm/gapfiller.rb +325 -0
- data/lib/finishm/orfs_finder.rb +88 -0
- data/lib/finishm/path_counter.rb +90 -0
- data/lib/finishm/primers.rb +425 -0
- data/lib/finishm/primers_check.rb +176 -0
- data/lib/finishm/roundup.rb +344 -0
- data/lib/finishm/sequence.rb +142 -0
- data/lib/finishm/visualise.rb +430 -0
- data/lib/finishm/wander.rb +270 -0
- data/lib/kmer_abundance_pattern.rb +79 -0
- data/lib/kmer_multi_abundance_file.rb +48 -0
- data/lib/oligo_designer.rb +88 -0
- data/lib/priner.rb +66 -0
- data/spec/acyclic_connection_finder_spec.rb +551 -0
- data/spec/all_orfs_spec.rb +443 -0
- data/spec/assemble_spec.rb +186 -0
- data/spec/bubbly_assembler_spec.rb +707 -0
- data/spec/c_node_finder_spec.rb +58 -0
- data/spec/connection_interpreter_spec.rb +284 -0
- data/spec/contig_printer_spec.rb +291 -0
- data/spec/coverage_based_graph_filter_spec.rb +102 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
- data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
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- data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
- data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
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- data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
- data/spec/data/assembly_visualiser/Graph +46 -0
- data/spec/data/assembly_visualiser/start_kmers1 +2 -0
- data/spec/data/bands.csv +1 -0
- data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq +0 -0
- data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
- data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
- data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
- data/spec/data/c_probe_node_finder/1/Log +756 -0
- data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
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- data/spec/data/contig_printer/1/seq.fa.svg +153 -0
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- data/spec/data/contig_printer/1/seq.fa.velvet/LastGraph +2953 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/PreGraph +27 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Sequences +3612 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/stats.txt +14 -0
- data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
- data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai +0 -0
- data/spec/data/contig_printer/1/seq.node12.fa +4 -0
- data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
- data/spec/data/contig_printer/1/seq2_1to550.fa +2 -0
- data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
- data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
- data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
- data/spec/data/explore/1/a.fa +2 -0
- data/spec/data/explore/1/seq1_and_a.fa +3 -0
- data/spec/data/explore/1/seq2.fa +2 -0
- data/spec/data/fluff/1/2seqs.sammy.fa +12004 -0
- data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
- data/spec/data/fluff/1/seq1.fa +2 -0
- data/spec/data/fluff/1/seq2.fa +2 -0
- data/spec/data/gapfilling/1/reads.fa +171 -0
- data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
- data/spec/data/gapfilling/1/velvetAssembly/Graph2 +130 -0
- data/spec/data/gapfilling/1/velvetAssembly/LastGraph +130 -0
- data/spec/data/gapfilling/1/velvetAssembly/Log +199 -0
- data/spec/data/gapfilling/1/velvetAssembly/PreGraph +7 -0
- data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
- data/spec/data/gapfilling/1/velvetAssembly/Sequences +281 -0
- data/spec/data/gapfilling/1/velvetAssembly/contigs.fa +12 -0
- data/spec/data/gapfilling/1/velvetAssembly/stats.txt +4 -0
- data/spec/data/gapfilling/2/HOWTO_recreate +17 -0
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- data/spec/data/gapfilling/2/sammy_reads.fa.gz +0 -0
- data/spec/data/gapfilling/2/with_gaps.fa +4 -0
- data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
- data/spec/data/gapfilling/3/reads.fa.gz +0 -0
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- data/spec/data/gapfilling/3/reference_part2.fa +4 -0
- data/spec/data/gapfilling/3/with_gaps.fa +4 -0
- data/spec/data/gapfilling/4/HOWTO_recreate +1 -0
- data/spec/data/gapfilling/4/reads.fa.gz +0 -0
- data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
- data/spec/data/gapfilling/5/answer.fna +2 -0
- data/spec/data/gapfilling/5/gappy.fna +2 -0
- data/spec/data/gapfilling/5/reads.fa +17961 -0
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- data/spec/data/gapfilling/6/reads.random2.fa.gz +0 -0
- data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
- data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
- data/spec/data/kmers_count1.csv +2 -0
- data/spec/data/kmers_count2.csv +3 -0
- data/spec/data/out +3 -0
- data/spec/data/positive_latching_pair.fa +2 -0
- data/spec/data/primers.csv +4 -0
- data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/input.fasta +6 -0
- data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
- data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.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
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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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* *
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* Efficient Memory Allocation Routines *
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* *
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* Guy St.C. Slater.. mailto:guy@ebi.ac.uk *
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* Copyright (C) 2000-2005. All Rights Reserved. *
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* *
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* This source code is distributed under the terms of the *
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* GNU Lesser General Public License. See the file COPYING *
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* or http://www.fsf.org/copyleft/lesser.html for details *
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* *
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\****************************************************************/
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#ifndef INCLUDED_RECYCLEBIN_H
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typedef struct recycleBin_st RecycleBin;
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void destroyRecycleBinArray(RecycleBin * recycle_bin);
|
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|
+
RecycleBin *getRecycleBinInArray(RecycleBin *recycleBin,
|
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|
+
int position);
|
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|
+
#endif
|
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|
+
|
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|
+
#endif /* INCLUDED_RECYCLEBIN_H */
|
@@ -0,0 +1,342 @@
|
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+
/*
|
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+
Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
|
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|
+
|
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|
+
This file is part of Velvet.
|
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|
+
|
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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
|
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,
|
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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.
|
15
|
+
|
16
|
+
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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|
+
|
20
|
+
*/
|
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|
+
#include <stdlib.h>
|
22
|
+
#include <string.h>
|
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|
+
#include <stdio.h>
|
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|
+
|
25
|
+
#include "globals.h"
|
26
|
+
#include "graph.h"
|
27
|
+
#include "recycleBin.h"
|
28
|
+
#include "tightString.h"
|
29
|
+
#include "roadMap.h"
|
30
|
+
#include "utility.h"
|
31
|
+
#include "kmer.h"
|
32
|
+
|
33
|
+
#ifndef NULL
|
34
|
+
#define NULL 0
|
35
|
+
#endif
|
36
|
+
|
37
|
+
union positionPtr {
|
38
|
+
ShortLength coord;
|
39
|
+
IDnum nodeID;
|
40
|
+
} ATTRIBUTE_PACKED;
|
41
|
+
|
42
|
+
struct annotation_st {
|
43
|
+
ShortLength position; // 32
|
44
|
+
union positionPtr start; // 32
|
45
|
+
union positionPtr finish; // 32
|
46
|
+
ShortLength length; // 32
|
47
|
+
IDnum sequenceID; // 32
|
48
|
+
} ATTRIBUTE_PACKED;
|
49
|
+
|
50
|
+
struct roadmap_st {
|
51
|
+
ShortLength annotationCount;
|
52
|
+
} ATTRIBUTE_PACKED;
|
53
|
+
|
54
|
+
IDnum getAnnotationCount(RoadMap * rdmap)
|
55
|
+
{
|
56
|
+
return rdmap->annotationCount;
|
57
|
+
}
|
58
|
+
|
59
|
+
Coordinate getFinish(Annotation * annot)
|
60
|
+
{
|
61
|
+
return annot->finish.coord;
|
62
|
+
}
|
63
|
+
|
64
|
+
IDnum getAnnotSequenceID(Annotation * annot)
|
65
|
+
{
|
66
|
+
return annot->sequenceID;
|
67
|
+
}
|
68
|
+
|
69
|
+
Coordinate getStart(Annotation * annot)
|
70
|
+
{
|
71
|
+
return annot->start.coord;
|
72
|
+
}
|
73
|
+
|
74
|
+
Coordinate getPosition(Annotation * annot)
|
75
|
+
{
|
76
|
+
return annot->position;
|
77
|
+
}
|
78
|
+
|
79
|
+
Coordinate getAnnotationLength(Annotation * annot)
|
80
|
+
{
|
81
|
+
if (annot == NULL)
|
82
|
+
return 0;
|
83
|
+
|
84
|
+
return annot->length;
|
85
|
+
}
|
86
|
+
|
87
|
+
//////////////////////////////////////////////////////////////
|
88
|
+
// Index conversion table
|
89
|
+
//////////////////////////////////////////////////////////////
|
90
|
+
|
91
|
+
//////////////////////////////////////////////////////////////
|
92
|
+
|
93
|
+
// Imports roadmap from the appropriate file format
|
94
|
+
// Memory allocated within the function
|
95
|
+
RoadMapArray *importRoadMapArray(char *filename)
|
96
|
+
{
|
97
|
+
FILE *file;
|
98
|
+
const int maxline = 100;
|
99
|
+
char *line = mallocOrExit(maxline, char);
|
100
|
+
RoadMap *rdmap = NULL;
|
101
|
+
IDnum seqID;
|
102
|
+
Coordinate position, start, finish;
|
103
|
+
Annotation *nextAnnotation;
|
104
|
+
RoadMapArray *result = mallocOrExit(1, RoadMapArray);
|
105
|
+
IDnum sequenceCount;
|
106
|
+
IDnum annotationCount = 0;
|
107
|
+
short short_var;
|
108
|
+
long long_var, long_var2;
|
109
|
+
long long longlong_var, longlong_var2, longlong_var3;
|
110
|
+
Coordinate *annotationOffset;
|
111
|
+
IDnum thisSeqID = 0;
|
112
|
+
|
113
|
+
velvetLog("Reading roadmap file %s\n", filename);
|
114
|
+
|
115
|
+
file = fopen(filename, "r");
|
116
|
+
if (!fgets(line, maxline, file))
|
117
|
+
exitErrorf(EXIT_FAILURE, true, "%s incomplete.", filename);
|
118
|
+
sscanf(line, "%ld\t%ld\t%i\t%hi\n", &long_var, &long_var2, &(result->WORDLENGTH), &short_var);
|
119
|
+
sequenceCount = (IDnum) long_var;
|
120
|
+
resetWordFilter(result->WORDLENGTH);
|
121
|
+
result->length = sequenceCount;
|
122
|
+
result->referenceCount = long_var2;
|
123
|
+
result->array = callocOrExit(sequenceCount, RoadMap);
|
124
|
+
result->double_strand = (boolean) short_var;
|
125
|
+
|
126
|
+
annotationOffset = callocOrExit(sequenceCount + 1, Coordinate);
|
127
|
+
while (fgets(line, maxline, file) != NULL)
|
128
|
+
{
|
129
|
+
if (line[0] != 'R')
|
130
|
+
{
|
131
|
+
annotationCount++;
|
132
|
+
annotationOffset[thisSeqID]++;
|
133
|
+
}
|
134
|
+
else
|
135
|
+
{
|
136
|
+
sscanf(line, "%*s %ld\n", &long_var);
|
137
|
+
thisSeqID = (IDnum) long_var;
|
138
|
+
}
|
139
|
+
}
|
140
|
+
|
141
|
+
result->annotations = callocOrExit(annotationCount, Annotation);
|
142
|
+
nextAnnotation = result->annotations;
|
143
|
+
fclose(file);
|
144
|
+
|
145
|
+
file = fopen(filename, "r");
|
146
|
+
|
147
|
+
// Cumulative sum
|
148
|
+
for (seqID = 1; seqID <= sequenceCount; seqID++)
|
149
|
+
annotationOffset[seqID] += annotationOffset[seqID - 1];
|
150
|
+
|
151
|
+
rdmap = result->array - 1;
|
152
|
+
if (!fgets(line, maxline, file))
|
153
|
+
exitErrorf(EXIT_FAILURE, true, "%s incomplete.", filename);
|
154
|
+
while (fgets(line, maxline, file) != NULL) {
|
155
|
+
if (line[0] == 'R') {
|
156
|
+
sscanf(line, "%*s %ld\n", &long_var);
|
157
|
+
thisSeqID = (IDnum) long_var;
|
158
|
+
nextAnnotation = result->annotations + annotationOffset[thisSeqID - 1];
|
159
|
+
rdmap = result->array + thisSeqID - 1;
|
160
|
+
} else {
|
161
|
+
sscanf(line, "%ld\t%lld\t%lld\t%lld\n", &long_var,
|
162
|
+
&longlong_var, &longlong_var2, &longlong_var3);
|
163
|
+
seqID = (IDnum) long_var;
|
164
|
+
position = (Coordinate) longlong_var;
|
165
|
+
start = (Coordinate) longlong_var2;
|
166
|
+
finish = (Coordinate) longlong_var3;
|
167
|
+
nextAnnotation->sequenceID = seqID;
|
168
|
+
nextAnnotation->position = position;
|
169
|
+
nextAnnotation->start.coord = start;
|
170
|
+
nextAnnotation->finish.coord = finish;
|
171
|
+
|
172
|
+
if (seqID > 0)
|
173
|
+
nextAnnotation->length = finish - start;
|
174
|
+
else
|
175
|
+
nextAnnotation->length = start - finish;
|
176
|
+
|
177
|
+
rdmap->annotationCount++;
|
178
|
+
nextAnnotation++;
|
179
|
+
}
|
180
|
+
}
|
181
|
+
velvetLog("%li roadmaps read\n", (long)sequenceCount);
|
182
|
+
|
183
|
+
free (annotationOffset);
|
184
|
+
fclose(file);
|
185
|
+
free(line);
|
186
|
+
return result;
|
187
|
+
}
|
188
|
+
|
189
|
+
// Imports roadmap for matches to reference from the appropriate file format
|
190
|
+
// Memory allocated within the function
|
191
|
+
RoadMapArray *importReferenceRoadMapArray(char *filename)
|
192
|
+
{
|
193
|
+
FILE *file;
|
194
|
+
const int maxline = 100;
|
195
|
+
char *line = mallocOrExit(maxline, char);
|
196
|
+
RoadMap *rdmap = NULL;
|
197
|
+
IDnum rdmapIndex = 0;
|
198
|
+
IDnum seqID;
|
199
|
+
Coordinate position, start, finish;
|
200
|
+
Annotation *nextAnnotation;
|
201
|
+
RoadMapArray *result = mallocOrExit(1, RoadMapArray);
|
202
|
+
IDnum sequenceCount;
|
203
|
+
IDnum annotationCount = 0;
|
204
|
+
short short_var;
|
205
|
+
long long_var, long_var2;
|
206
|
+
long long longlong_var, longlong_var2, longlong_var3;
|
207
|
+
Coordinate *annotationOffset;
|
208
|
+
IDnum thisSeqID = 0;
|
209
|
+
|
210
|
+
velvetLog("Reading roadmap file %s\n", filename);
|
211
|
+
|
212
|
+
file = fopen(filename, "r");
|
213
|
+
if (!fgets(line, maxline, file))
|
214
|
+
exitErrorf(EXIT_FAILURE, true, "%s incomplete.", filename);
|
215
|
+
sscanf(line, "%ld\t%ld\t%i\t%hi\n", &long_var, &long_var2, &(result->WORDLENGTH), &short_var);
|
216
|
+
sequenceCount = (IDnum) long_var;
|
217
|
+
resetWordFilter(result->WORDLENGTH);
|
218
|
+
result->length = sequenceCount;
|
219
|
+
result->referenceCount = long_var2;
|
220
|
+
result->array = callocOrExit(sequenceCount, RoadMap);
|
221
|
+
result->double_strand = (boolean) short_var;
|
222
|
+
|
223
|
+
annotationOffset = callocOrExit(sequenceCount + 1, Coordinate);
|
224
|
+
while (fgets(line, maxline, file) != NULL)
|
225
|
+
{
|
226
|
+
if (line[0] != 'R')
|
227
|
+
{
|
228
|
+
sscanf(line, "%ld\t%lld\t%lld\t%lld\n", &long_var,
|
229
|
+
&longlong_var, &longlong_var2, &longlong_var3);
|
230
|
+
seqID = (IDnum) long_var;
|
231
|
+
if (seqID <= result->referenceCount && seqID >= -result->referenceCount)
|
232
|
+
{
|
233
|
+
annotationCount++;
|
234
|
+
annotationOffset[thisSeqID]++;
|
235
|
+
}
|
236
|
+
}
|
237
|
+
else
|
238
|
+
{
|
239
|
+
sscanf(line, "%*s %ld\n", &long_var);
|
240
|
+
thisSeqID = (IDnum) long_var;
|
241
|
+
}
|
242
|
+
}
|
243
|
+
|
244
|
+
result->annotations = callocOrExit(annotationCount, Annotation);
|
245
|
+
nextAnnotation = result->annotations;
|
246
|
+
fclose(file);
|
247
|
+
|
248
|
+
file = fopen(filename, "r");
|
249
|
+
|
250
|
+
// Cumulative sum
|
251
|
+
for (seqID = 1; seqID <= sequenceCount; seqID++)
|
252
|
+
annotationOffset[seqID] += annotationOffset[seqID - 1];
|
253
|
+
|
254
|
+
rdmap = result->array - 1;
|
255
|
+
if (!fgets(line, maxline, file))
|
256
|
+
exitErrorf(EXIT_FAILURE, true, "%s incomplete.", filename);
|
257
|
+
while (fgets(line, maxline, file) != NULL) {
|
258
|
+
if (line[0] == 'R') {
|
259
|
+
sscanf(line, "%*s %ld\n", &long_var);
|
260
|
+
thisSeqID = (IDnum) long_var;
|
261
|
+
nextAnnotation = result->annotations + annotationOffset[thisSeqID - 1];
|
262
|
+
rdmap = result->array + thisSeqID - 1;
|
263
|
+
rdmapIndex++;
|
264
|
+
} else {
|
265
|
+
sscanf(line, "%ld\t%lld\t%lld\t%lld\n", &long_var,
|
266
|
+
&longlong_var, &longlong_var2, &longlong_var3);
|
267
|
+
seqID = (IDnum) long_var;
|
268
|
+
if (seqID <= result->referenceCount && seqID >= -result->referenceCount)
|
269
|
+
{
|
270
|
+
position = (Coordinate) longlong_var;
|
271
|
+
start = (Coordinate) longlong_var2;
|
272
|
+
finish = (Coordinate) longlong_var3;
|
273
|
+
nextAnnotation->sequenceID = seqID;
|
274
|
+
nextAnnotation->position = position;
|
275
|
+
nextAnnotation->start.coord = start;
|
276
|
+
nextAnnotation->finish.coord = finish;
|
277
|
+
|
278
|
+
if (seqID > 0)
|
279
|
+
nextAnnotation->length = finish - start;
|
280
|
+
else
|
281
|
+
nextAnnotation->length = start - finish;
|
282
|
+
|
283
|
+
rdmap->annotationCount++;
|
284
|
+
nextAnnotation++;
|
285
|
+
}
|
286
|
+
}
|
287
|
+
}
|
288
|
+
|
289
|
+
velvetLog("%li roadmaps references\n", (long) rdmapIndex);
|
290
|
+
|
291
|
+
free(annotationOffset);
|
292
|
+
fclose(file);
|
293
|
+
free(line);
|
294
|
+
return result;
|
295
|
+
}
|
296
|
+
|
297
|
+
RoadMap *getRoadMapInArray(RoadMapArray * array, IDnum index)
|
298
|
+
{
|
299
|
+
return array->array + index;
|
300
|
+
}
|
301
|
+
|
302
|
+
void setStartID(Annotation * annot, IDnum nodeID)
|
303
|
+
{
|
304
|
+
annot->start.nodeID = nodeID;
|
305
|
+
}
|
306
|
+
|
307
|
+
void setFinishID(Annotation * annot, IDnum nodeID)
|
308
|
+
{
|
309
|
+
annot->finish.nodeID = nodeID;
|
310
|
+
}
|
311
|
+
|
312
|
+
IDnum getStartID(Annotation * annot)
|
313
|
+
{
|
314
|
+
return annot->start.nodeID;
|
315
|
+
}
|
316
|
+
|
317
|
+
IDnum getFinishID(Annotation * annot)
|
318
|
+
{
|
319
|
+
return annot->finish.nodeID;
|
320
|
+
}
|
321
|
+
|
322
|
+
void incrementAnnotationCoordinates(Annotation * annot)
|
323
|
+
{
|
324
|
+
annot->start.coord++;
|
325
|
+
annot->finish.coord++;
|
326
|
+
}
|
327
|
+
|
328
|
+
Annotation *getNextAnnotation(Annotation * annot)
|
329
|
+
{
|
330
|
+
return annot + 1;
|
331
|
+
}
|
332
|
+
|
333
|
+
Annotation *getAnnotationInArray(Annotation * annot, Coordinate index)
|
334
|
+
{
|
335
|
+
return annot + index;
|
336
|
+
}
|
337
|
+
|
338
|
+
void destroyRoadMapArray(RoadMapArray * rdmaps) {
|
339
|
+
free(rdmaps->array);
|
340
|
+
free(rdmaps->annotations);
|
341
|
+
free(rdmaps);
|
342
|
+
}
|
@@ -0,0 +1,65 @@
|
|
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 _ROADMAP_H_
|
22
|
+
#define _ROADMAP_H_
|
23
|
+
|
24
|
+
#include <stdio.h>
|
25
|
+
|
26
|
+
struct roadMapArray_st {
|
27
|
+
RoadMap *array;
|
28
|
+
Annotation *annotations;
|
29
|
+
IDnum length;
|
30
|
+
int WORDLENGTH;
|
31
|
+
boolean double_strand;
|
32
|
+
IDnum referenceCount;
|
33
|
+
};
|
34
|
+
|
35
|
+
////////////////////////////////////////////////////////////////////
|
36
|
+
// Annotation stuff
|
37
|
+
////////////////////////////////////////////////////////////////////
|
38
|
+
IDnum getAnnotSequenceID(Annotation * annot);
|
39
|
+
Coordinate getFinish(Annotation * annot);
|
40
|
+
Coordinate getStart(Annotation * annot);
|
41
|
+
Coordinate getPosition(Annotation * annot);
|
42
|
+
Coordinate getAnnotationLength(Annotation * annot);
|
43
|
+
void incrementAnnotationCoordinates(Annotation * annot);
|
44
|
+
|
45
|
+
void setStartID(Annotation * annot, IDnum nodeID);
|
46
|
+
IDnum getStartID(Annotation * annot);
|
47
|
+
void setFinishID(Annotation * annot, IDnum nodeID);
|
48
|
+
IDnum getFinishID(Annotation * annot);
|
49
|
+
|
50
|
+
Annotation *getNextAnnotation(Annotation * annot);
|
51
|
+
Annotation *getAnnotationInArray(Annotation * annot, Coordinate index);
|
52
|
+
|
53
|
+
////////////////////////////////////////////////////////////////////
|
54
|
+
// RoadMap stuff
|
55
|
+
////////////////////////////////////////////////////////////////////
|
56
|
+
|
57
|
+
IDnum getAnnotationCount(RoadMap * rdmap);
|
58
|
+
|
59
|
+
RoadMap *getRoadMapInArray(RoadMapArray * array, IDnum index);
|
60
|
+
|
61
|
+
// Same thing but for the RoadMap file generated by the hash
|
62
|
+
RoadMapArray *importRoadMapArray(char *filename);
|
63
|
+
RoadMapArray *importReferenceRoadMapArray(char * filename);
|
64
|
+
void destroyRoadMapArray(RoadMapArray * rdmap);
|
65
|
+
#endif
|