bio-velvet_underground 0.0.1
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- checksums.yaml +7 -0
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- data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
- data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
- data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
- data/lib/bio-velvet_underground.rb +12 -0
- data/lib/bio-velvet_underground/external/VERSION +1 -0
- data/lib/bio-velvet_underground/velvet_underground.rb +72 -0
- data/spec/binary_sequence_store_spec.rb +27 -0
- data/spec/data/1/CnyUnifiedSeq +0 -0
- data/spec/spec_helper.rb +31 -0
- metadata +456 -0
@@ -0,0 +1,26 @@
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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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#ifndef _PREGRAPHCONSTRUCTION_H_
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#define _PREGRAPHCONSTRUCTION_H_
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PreGraph *newPreGraph_pg(RoadMapArray * rdmaps, SequencesReader *seqReadInfo);
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#endif
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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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+
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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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#include <stdlib.h>
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#include <stdio.h>
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#include "globals.h"
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#include "graph.h"
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#include "recycleBin.h"
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#include "passageMarker.h"
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#include "graphStats.h"
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#include "concatenatedGraph.h"
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#include "readSet.h"
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#include "utility.h"
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#define LONG_NODE_CUTOFF 50
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#define LN2 0.693147
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#define PROBABILITY_CUTOFF 5
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#define MAX_READ_COUNT 100
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#define MAX_READ_LENGTH 2000
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static Graph *graph = NULL;
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static PassageMarkerI path = NULL_IDX;
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static RecycleBin *listMemory = NULL;
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static double expected_coverage = 1;
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static TightString *sequences = NULL;
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static int MULTIPLICITY_CUTOFF = 2;
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+
|
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static IDnum multCounter = 0;
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static IDnum dbgCounter = 0;
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static IDnum nullCounter = 0;
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typedef struct rb_connection_st RBConnection;
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51
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struct rb_connection_st {
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Node *node;
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PassageMarkerI marker;
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RBConnection *next;
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IDnum multiplicity;
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} ATTRIBUTE_PACKED;
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+
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static RecycleBin *nodeListMemory = NULL;
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#define BLOCKSIZE 1000
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static RBConnection *allocateRBConnection()
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{
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if (nodeListMemory == NULL)
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nodeListMemory =
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newRecycleBin(sizeof(RBConnection), BLOCKSIZE);
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return allocatePointer(nodeListMemory);
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}
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static void deallocateRBConnection(RBConnection * nodeList)
|
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{
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deallocatePointer(nodeListMemory, nodeList);
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}
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boolean isUniqueSolexa(Node * node)
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{
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Coordinate nodeLength = getNodeLength(node);
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Coordinate nodeCoverage;
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double nodeDensity, probability;
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nodeCoverage = getTotalCoverage(node);
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if (nodeLength > LONG_NODE_CUTOFF) {
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nodeDensity = nodeCoverage / (double) nodeLength;
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probability =
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LN2 / 2 +
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nodeLength / (2 * expected_coverage) *
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(expected_coverage * expected_coverage -
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nodeDensity * nodeDensity / 2);
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return probability > PROBABILITY_CUTOFF;
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}
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return false;
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}
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static void identifyUniqueNodes(boolean(*isUniqueFunction) (Node *))
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{
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IDnum index;
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Node *node;
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IDnum counter = 0;
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velvetLog("Identifying unique nodes\n");
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for (index = 1; index <= nodeCount(graph); index++) {
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node = getNodeInGraph(graph, index);
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if (node == NULL)
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continue;
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setUniqueness(node, isUniqueFunction(node));
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if (getUniqueness(node))
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counter++;
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}
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velvetLog("Done, %li unique nodes counted\n", (long) counter);
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}
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static boolean uniqueNodesConnect(Node * startingNode)
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{
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Node *destination = NULL;
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PassageMarkerI startMarker, currentMarker;
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RBConnection *newList;
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RBConnection *list = NULL;
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boolean multipleHits = false;
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if (arcCount(startingNode) == 0)
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return false;
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if (getMarker(startingNode) == NULL_IDX)
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return false;
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135
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dbgCounter++;
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137
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138
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// Checking for multiple destinations
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for (startMarker = getMarker(startingNode); startMarker != NULL_IDX;
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startMarker = getNextInNode(startMarker)) {
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if (getFinishOffset(startMarker) >
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2 * getWordLength(graph))
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continue;
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for (currentMarker = getNextInSequence(startMarker);
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currentMarker != NULL_IDX;
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currentMarker = getNextInSequence(currentMarker)) {
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if (!getUniqueness(getNode(currentMarker))) {
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continue;
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} else if (getNodeStatus(getNode(currentMarker))) {
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if (getStartOffset(currentMarker) >
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2 * getWordLength(graph))
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break;
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for (newList = list; newList != NULL;
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newList = newList->next) {
|
156
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if (newList->node ==
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getNode(currentMarker)) {
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newList->multiplicity++;
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break;
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}
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}
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if (newList == NULL)
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abort();
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break;
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} else {
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if (getStartOffset(currentMarker) >
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2 * getWordLength(graph))
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break;
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setSingleNodeStatus(getNode(currentMarker),
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true);
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newList = allocateRBConnection();
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newList->node = getNode(currentMarker);
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173
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newList->multiplicity = 1;
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newList->marker = startMarker;
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newList->next = list;
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list = newList;
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break;
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}
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179
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}
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}
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181
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while (list != NULL) {
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newList = list;
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list = newList->next;
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setSingleNodeStatus(newList->node, false);
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186
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if (newList->multiplicity >= MULTIPLICITY_CUTOFF) {
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187
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if (destination == NULL) {
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destination = newList->node;
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path = newList->marker;
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190
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} else if (destination != newList->node)
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191
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multipleHits = true;
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192
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}
|
193
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deallocateRBConnection(newList);
|
194
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}
|
195
|
+
|
196
|
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if (multipleHits) {
|
197
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multCounter++;
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setUniqueness(startingNode, false);
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return false;
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200
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}
|
201
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|
202
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if (destination == NULL || destination == startingNode
|
203
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|| destination == getTwinNode(startingNode)) {
|
204
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nullCounter++;
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205
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return false;
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206
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}
|
207
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// Check for reciprocity
|
208
|
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for (startMarker = getMarker(getTwinNode(destination));
|
209
|
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startMarker != NULL_IDX;
|
210
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startMarker = getNextInNode(startMarker)) {
|
211
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if (getFinishOffset(startMarker) >
|
212
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2 * getWordLength(graph))
|
213
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continue;
|
214
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+
|
215
|
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for (currentMarker = getNextInSequence(startMarker);
|
216
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currentMarker != NULL_IDX;
|
217
|
+
currentMarker = getNextInSequence(currentMarker)) {
|
218
|
+
if (!getUniqueness(getNode(currentMarker))) {
|
219
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continue;
|
220
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+
} else if (getNodeStatus(getNode(currentMarker))) {
|
221
|
+
if (getStartOffset(currentMarker) >
|
222
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2 * getWordLength(graph))
|
223
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break;
|
224
|
+
for (newList = list; newList != NULL;
|
225
|
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newList = newList->next) {
|
226
|
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if (newList->node ==
|
227
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getNode(currentMarker)) {
|
228
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+
newList->multiplicity++;
|
229
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+
break;
|
230
|
+
}
|
231
|
+
}
|
232
|
+
if (newList == NULL)
|
233
|
+
abort();
|
234
|
+
break;
|
235
|
+
} else {
|
236
|
+
if (getStartOffset(currentMarker) >
|
237
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+
2 * getWordLength(graph))
|
238
|
+
break;
|
239
|
+
setSingleNodeStatus(getNode(currentMarker),
|
240
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+
true);
|
241
|
+
newList = allocateRBConnection();
|
242
|
+
newList->node = getNode(currentMarker);
|
243
|
+
newList->multiplicity = 1;
|
244
|
+
newList->next = list;
|
245
|
+
list = newList;
|
246
|
+
break;
|
247
|
+
}
|
248
|
+
}
|
249
|
+
}
|
250
|
+
|
251
|
+
while (list != NULL) {
|
252
|
+
newList = list;
|
253
|
+
list = newList->next;
|
254
|
+
setSingleNodeStatus(newList->node, false);
|
255
|
+
if (newList->multiplicity >= MULTIPLICITY_CUTOFF
|
256
|
+
&& newList->node != getTwinNode(startingNode))
|
257
|
+
multipleHits = true;
|
258
|
+
deallocateRBConnection(newList);
|
259
|
+
}
|
260
|
+
|
261
|
+
if (multipleHits) {
|
262
|
+
multCounter++;
|
263
|
+
setUniqueness(destination, false);
|
264
|
+
return false;
|
265
|
+
}
|
266
|
+
// Aligning long reads to each other:
|
267
|
+
// TODO
|
268
|
+
|
269
|
+
// Merge pairwise alignments and produce consensus
|
270
|
+
// TODO
|
271
|
+
|
272
|
+
return true;
|
273
|
+
}
|
274
|
+
|
275
|
+
static boolean goesToNode(PassageMarkerI marker, Node * node)
|
276
|
+
{
|
277
|
+
PassageMarkerI current;
|
278
|
+
Node * start = getNode(marker);
|
279
|
+
Node * twinStart = getTwinNode(start);
|
280
|
+
Node * currentNode;
|
281
|
+
|
282
|
+
for (current = getNextInSequence(marker); current != NULL_IDX;
|
283
|
+
current = getNextInSequence(current)) {
|
284
|
+
currentNode = getNode(current);
|
285
|
+
if (currentNode == start || currentNode == twinStart)
|
286
|
+
return false;
|
287
|
+
else if (currentNode == node)
|
288
|
+
return true;
|
289
|
+
else if (getUniqueness(currentNode))
|
290
|
+
return false;
|
291
|
+
}
|
292
|
+
|
293
|
+
return false;
|
294
|
+
}
|
295
|
+
|
296
|
+
static void updateMembers(Node * bypass, Node * nextNode)
|
297
|
+
{
|
298
|
+
PassageMarkerI marker, next, tmp;
|
299
|
+
Coordinate nextLength = getNodeLength(nextNode);
|
300
|
+
|
301
|
+
// Update marker + arc info
|
302
|
+
for (marker = getMarker(bypass); marker != NULL_IDX; marker = tmp) {
|
303
|
+
tmp = getNextInNode(marker);
|
304
|
+
|
305
|
+
if (!isTerminal(marker)
|
306
|
+
&& getNode(getNextInSequence(marker)) == nextNode) {
|
307
|
+
// Marker steps right into target
|
308
|
+
next = getNextInSequence(marker);
|
309
|
+
disconnectNextPassageMarker(marker, graph);
|
310
|
+
destroyPassageMarker(next);
|
311
|
+
} else if (getUniqueness(nextNode)
|
312
|
+
&& goesToNode(marker, nextNode)) {
|
313
|
+
// Marker goes indirectly to target
|
314
|
+
while (getNode(getNextInSequence(marker)) !=
|
315
|
+
nextNode) {
|
316
|
+
next = getNextInSequence(marker);
|
317
|
+
disconnectNextPassageMarker(marker, graph);
|
318
|
+
destroyPassageMarker(next);
|
319
|
+
}
|
320
|
+
|
321
|
+
next = getNextInSequence(marker);
|
322
|
+
disconnectNextPassageMarker(marker, graph);
|
323
|
+
destroyPassageMarker(next);
|
324
|
+
} else if (!isTerminal(marker)
|
325
|
+
&& getFinishOffset(marker) == 0) {
|
326
|
+
// Marker goes somewhere else than to target
|
327
|
+
next = getNextInSequence(marker);
|
328
|
+
incrementFinishOffset(marker, nextLength);
|
329
|
+
} else {
|
330
|
+
// Marker goes nowhere
|
331
|
+
incrementFinishOffset(marker, nextLength);
|
332
|
+
}
|
333
|
+
}
|
334
|
+
}
|
335
|
+
|
336
|
+
static void admitGroupies(Node * source, Node * bypass)
|
337
|
+
{
|
338
|
+
PassageMarkerI marker, tmpMarker;
|
339
|
+
|
340
|
+
for (marker = getMarker(source); marker != NULL_IDX;
|
341
|
+
marker = tmpMarker) {
|
342
|
+
tmpMarker = getNextInNode(marker);
|
343
|
+
extractPassageMarker(marker);
|
344
|
+
transposePassageMarker(marker, bypass);
|
345
|
+
incrementFinishOffset(getTwinMarker(marker),
|
346
|
+
getNodeLength(bypass));
|
347
|
+
}
|
348
|
+
|
349
|
+
}
|
350
|
+
|
351
|
+
static void adjustShortReads(Node * target, PassageMarkerI pathMarker)
|
352
|
+
{
|
353
|
+
ShortReadMarker *targetArray, *marker;
|
354
|
+
IDnum targetLength, index;
|
355
|
+
Coordinate position, nodeLength;
|
356
|
+
|
357
|
+
if (!readStartsAreActivated(graph))
|
358
|
+
return;
|
359
|
+
|
360
|
+
targetArray = getNodeReads(getTwinNode(target), graph);
|
361
|
+
targetLength = getNodeReadCount(getTwinNode(target), graph);
|
362
|
+
|
363
|
+
nodeLength = getPassageMarkerLength(pathMarker);
|
364
|
+
|
365
|
+
for (index = 0; index < targetLength; index++) {
|
366
|
+
marker = getShortReadMarkerAtIndex(targetArray, index);
|
367
|
+
position = getShortReadMarkerPosition(marker);
|
368
|
+
position += nodeLength;
|
369
|
+
setShortReadMarkerPosition(marker, position);
|
370
|
+
}
|
371
|
+
}
|
372
|
+
|
373
|
+
static Node *bypass()
|
374
|
+
{
|
375
|
+
Node *bypass = getNode(path);
|
376
|
+
Node *next = NULL;
|
377
|
+
Arc *arc;
|
378
|
+
PassageMarkerI nextMarker;
|
379
|
+
|
380
|
+
// Remove unwanted arcs
|
381
|
+
while (getArc(bypass) != NULL)
|
382
|
+
destroyArc(getArc(bypass), graph);
|
383
|
+
|
384
|
+
// Update extensive variables (length + descriptors + passage markers)
|
385
|
+
while (!isTerminal(path)) {
|
386
|
+
nextMarker = getNextInSequence(path);
|
387
|
+
next = getNode(nextMarker);
|
388
|
+
while (next == bypass) {
|
389
|
+
disconnectNextPassageMarker(path, graph);
|
390
|
+
destroyPassageMarker(nextMarker);
|
391
|
+
nextMarker = getNextInSequence(path);
|
392
|
+
next = getNode(nextMarker);
|
393
|
+
}
|
394
|
+
|
395
|
+
if (next == NULL)
|
396
|
+
return bypass;
|
397
|
+
|
398
|
+
// Overall node update
|
399
|
+
if (!getUniqueness(next)) {
|
400
|
+
adjustShortReads(bypass, getNextInSequence(path));
|
401
|
+
appendSequence(bypass, sequences,
|
402
|
+
getNextInSequence(path), graph);
|
403
|
+
} else {
|
404
|
+
concatenateReadStarts(bypass, next, graph);
|
405
|
+
|
406
|
+
#ifndef SINGLE_COV_CAT
|
407
|
+
Category cat;
|
408
|
+
for (cat = 0; cat < CATEGORIES; cat++) {
|
409
|
+
// Update virtual coverage
|
410
|
+
incrementVirtualCoverage(bypass, cat,
|
411
|
+
getVirtualCoverage(next, cat));
|
412
|
+
// Update original virtual coverage
|
413
|
+
incrementOriginalVirtualCoverage(bypass, cat,
|
414
|
+
getOriginalVirtualCoverage(next, cat));
|
415
|
+
}
|
416
|
+
#else
|
417
|
+
incrementVirtualCoverage(bypass, getVirtualCoverage(next));
|
418
|
+
#endif
|
419
|
+
appendDescriptors(bypass, next);
|
420
|
+
}
|
421
|
+
|
422
|
+
// Members
|
423
|
+
updateMembers(bypass, next);
|
424
|
+
|
425
|
+
// Termination
|
426
|
+
if (isTerminal(path) || getUniqueness(next))
|
427
|
+
break;
|
428
|
+
}
|
429
|
+
|
430
|
+
// Remove unique groupies from arrival
|
431
|
+
admitGroupies(next, bypass);
|
432
|
+
|
433
|
+
// Copy destination arcs
|
434
|
+
for (arc = getArc(next); arc != NULL; arc = getNextArc(arc)) {
|
435
|
+
if (getDestination(arc) == next)
|
436
|
+
continue;
|
437
|
+
else if (getDestination(arc) == getTwinNode(next))
|
438
|
+
createAnalogousArc(bypass, getTwinNode(bypass),
|
439
|
+
arc, graph);
|
440
|
+
else
|
441
|
+
createAnalogousArc(bypass, getDestination(arc),
|
442
|
+
arc, graph);
|
443
|
+
}
|
444
|
+
|
445
|
+
destroyNode(next, graph);
|
446
|
+
|
447
|
+
return bypass;
|
448
|
+
}
|
449
|
+
|
450
|
+
static void trimLongReadTips()
|
451
|
+
{
|
452
|
+
IDnum index;
|
453
|
+
Node *node;
|
454
|
+
PassageMarkerI marker, next;
|
455
|
+
|
456
|
+
velvetLog("Trimming read tips\n");
|
457
|
+
|
458
|
+
for (index = 1; index <= nodeCount(graph); index++) {
|
459
|
+
node = getNodeInGraph(graph, index);
|
460
|
+
|
461
|
+
if (getUniqueness(node))
|
462
|
+
continue;
|
463
|
+
|
464
|
+
for (marker = getMarker(node); marker != NULL_IDX;
|
465
|
+
marker = next) {
|
466
|
+
next = getNextInNode(marker);
|
467
|
+
|
468
|
+
if (!isInitial(marker) && !isTerminal(marker))
|
469
|
+
continue;
|
470
|
+
|
471
|
+
if (isTerminal(marker))
|
472
|
+
marker = getTwinMarker(marker);
|
473
|
+
|
474
|
+
while (!getUniqueness(getNode(marker))) {
|
475
|
+
if (next != NULL_IDX
|
476
|
+
&& (marker == next
|
477
|
+
|| marker == getTwinMarker(next)))
|
478
|
+
next = getNextInNode(next);
|
479
|
+
if (getNextInSequence(marker) != NULL_IDX) {
|
480
|
+
marker = getNextInSequence(marker);
|
481
|
+
destroyPassageMarker
|
482
|
+
(getPreviousInSequence
|
483
|
+
(marker));
|
484
|
+
} else {
|
485
|
+
destroyPassageMarker(marker);
|
486
|
+
break;
|
487
|
+
}
|
488
|
+
}
|
489
|
+
}
|
490
|
+
}
|
491
|
+
}
|
492
|
+
|
493
|
+
void readCoherentGraph(Graph * inGraph, boolean(*isUnique) (Node * node),
|
494
|
+
double coverage, ReadSet * reads)
|
495
|
+
{
|
496
|
+
IDnum nodeIndex;
|
497
|
+
Node *node;
|
498
|
+
IDnum previousNodeCount = 0;
|
499
|
+
|
500
|
+
graph = inGraph;
|
501
|
+
listMemory = newRecycleBin(sizeof(PassageMarkerList), 100000);
|
502
|
+
expected_coverage = coverage;
|
503
|
+
sequences = reads->tSequences;
|
504
|
+
|
505
|
+
velvetLog("Read coherency...\n");
|
506
|
+
resetNodeStatus(graph);
|
507
|
+
identifyUniqueNodes(isUnique);
|
508
|
+
trimLongReadTips();
|
509
|
+
|
510
|
+
previousNodeCount = 0;
|
511
|
+
while (previousNodeCount != nodeCount(graph)) {
|
512
|
+
|
513
|
+
previousNodeCount = nodeCount(graph);
|
514
|
+
|
515
|
+
for (nodeIndex = 1; nodeIndex <= nodeCount(graph);
|
516
|
+
nodeIndex++) {
|
517
|
+
|
518
|
+
node = getNodeInGraph(graph, nodeIndex);
|
519
|
+
|
520
|
+
if (node == NULL || !getUniqueness(node))
|
521
|
+
continue;
|
522
|
+
|
523
|
+
while (uniqueNodesConnect(node))
|
524
|
+
node = bypass();
|
525
|
+
|
526
|
+
node = getTwinNode(node);
|
527
|
+
|
528
|
+
while (uniqueNodesConnect(node))
|
529
|
+
node = bypass();
|
530
|
+
|
531
|
+
}
|
532
|
+
|
533
|
+
renumberNodes(graph);
|
534
|
+
}
|
535
|
+
|
536
|
+
destroyRecycleBin(listMemory);
|
537
|
+
destroyRecycleBin(nodeListMemory);
|
538
|
+
|
539
|
+
velvetLog("Confronted to %li multiple hits and %li null over %li\n",
|
540
|
+
(long) multCounter, (long) nullCounter, (long) dbgCounter);
|
541
|
+
|
542
|
+
velvetLog("Read coherency over!\n");
|
543
|
+
}
|
544
|
+
|
545
|
+
void setMultiplicityCutoff(int value)
|
546
|
+
{
|
547
|
+
if (value < 0) {
|
548
|
+
velvetLog("Negative long read multiplicity cutoff %i!\n",
|
549
|
+
value);
|
550
|
+
velvetLog("Exiting...\n");
|
551
|
+
#ifdef DEBUG
|
552
|
+
abort();
|
553
|
+
#endif
|
554
|
+
exit(1);
|
555
|
+
}
|
556
|
+
MULTIPLICITY_CUTOFF = value;
|
557
|
+
}
|