bio-velvet_underground 0.0.1

data/ext/src/src/graphStats.h

@@ -0,0 +1,72 @@
+/*
+Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#ifndef _GRAPHSTATS_H_
+#define _GRAPHSTATS_H_
+
+
+void displayGeneralStatistics(Graph * graph, char *filename, ReadSet * reads);
+
+void exportLongNodeSequences(char *filename, Graph * graph,
+			     Coordinate minLength, ReadSet * reads, ShortLength * readLengths, IDnum minCov);
+
+Coordinate readCoverage(Node * node);
+
+Coordinate n50(Graph * graph);
+
+double estimated_cov(Graph * graph, char * directory);
+
+Coordinate maxLength(Graph * graph);
+
+boolean *removeLowCoverageNodesAndDenounceDubiousReads(Graph * graph,
+						       double minCov,
+						       ReadSet * reads,
+						       boolean export,
+						       Coordinate minLength,
+						       char *filename);
+
+void removeLowLongCoverageNodesAndDenounceDubiousReads(Graph * graph,
+						       double minCov,
+						       ReadSet * reads,
+						       boolean * dubious,
+						       boolean export,
+						       Coordinate minLength,
+						       char *filename);
+
+void removeLowCoverageReferenceNodes(Graph * graph, double minCov, double minLongCov, ReadSet * reads);
+
+void exportAMOSContigs(char *filename, Graph * graph,
+		       Coordinate cutoff_length, ReadSet * reads);
+
+IDnum usedReads(Graph * graph, Coordinate minContigLength); 
+
+Coordinate totalAssemblyLength(Graph * graph);
+
+void logFinalStats(Graph * graph, Coordinate minContigKmerLength, char *directory);
+
+void exportUnusedReads(Graph* graph, ReadSet * reads, Coordinate minContigKmerLength, char* filename);
+
+void exportLongNodeMappings(char *filename, Graph * graph, ReadSet * reads,
+			     Coordinate minLength, SequencesReader *seqReadInfo);
+
+void removeHighCoverageNodes(Graph * graph, double maxCov, boolean export, Coordinate minLength, char * filename);
+
+void removeLowArcs(Graph * graph, double cutoff);
+#endif

data/ext/src/src/kmer.c

@@ -0,0 +1,652 @@
+/*
+Copyright 2007, 2008, 2009 Daniel Zerbino (zerbino@ebi.ac.uk)
+
+    This file is part of Velvet.
+
+    Velvet is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    Velvet is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Velvet; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+*/
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "globals.h"
+#include "kmer.h"
+#include "utility.h"
+
+static const uint64_t longLongLeftFilter = (uint64_t) 3 << 62; 
+static const uint32_t longLeftFilter = (uint32_t) 3 << 30; 
+static const uint16_t intLeftFilter = (uint16_t) 3 << 14; 
+static const uint8_t charLeftFilter = (uint8_t) 3 << 6; 
+
+#if KMER_LONGLONGS
+static uint64_t longLongWordFilter = (uint64_t) ((int64_t) -1); 
+#endif
+static uint32_t longWordFilter = (uint32_t) ((int32_t) -1); 
+static uint16_t intWordFilter = (uint16_t) ((int16_t) -1); 
+static uint8_t charWordFilter = (uint8_t) ((int8_t) -1); 
+
+#define UNDEFINED 0
+#define CHARS 1
+#define INTS 2
+#define LONGS 3
+#define LONGLONGS 4
+static int kmerFilterIndex = UNDEFINED;
+static int kmerFilterOffset = 0;
+static int kmerFilterLength = 0;
+#if KMER_LONGLONGS
+static int longLongKmerFilterIndex = KMER_LONGLONGS - 1;
+static uint64_t longLongKmerFilter = (uint64_t) ((int64_t) -1); 
+#endif
+
+static uint64_t keyFilter = 0;
+static int keyFilterIndex = UNDEFINED;
+static int keyFilterOffset = 0;
+static int keyFilterLength = 0;
+#if KMER_LONGLONGS
+static int longLongKeyFilterIndex = KMER_LONGLONGS - 1;
+#endif
+
+void resetWordFilter(int wordLength) {
+	int kmer_bit_size = wordLength * 2;
+
+	if (wordLength > MAXKMERLENGTH) 
+		exitErrorf(EXIT_FAILURE, true, "Word length %i greater than max allowed value (%i).\nRecompile Velvet to deal with this word length.", wordLength, MAXKMERLENGTH);
+
+#if KMER_LONGLONGS
+	int i;
+	for (i = 0; i < KMER_LONGLONGS; i++) {
+		if (kmer_bit_size > 64) {
+			kmer_bit_size -= 64;
+			continue;
+		} else if (kmer_bit_size == 64) {
+			longLongKmerFilterIndex = i;
+			longLongKmerFilter = longLongWordFilter; 
+			kmerFilterIndex = LONGLONGS;
+			kmerFilterOffset = kmer_bit_size - 2;
+			kmerFilterLength = kmer_bit_size;
+			longWordFilter = 0;
+			intWordFilter = 0;
+			charWordFilter = 0;
+			return;
+		} else {
+			longLongKmerFilterIndex = i;
+			longLongKmerFilter = (((uint64_t) 1) << kmer_bit_size) - 1;	
+			kmerFilterIndex = LONGLONGS;
+			kmerFilterOffset = kmer_bit_size - 2;
+			kmerFilterLength = kmer_bit_size;
+			longWordFilter = 0;
+			intWordFilter = 0;
+			charWordFilter = 0;
+			return;
+		}
+	}
+#endif
+#if KMER_LONGS
+	if (kmer_bit_size > 32)
+		kmer_bit_size -= 32;
+	else if (kmer_bit_size == 32) {
+		kmerFilterIndex = LONGS;
+		kmerFilterOffset = kmer_bit_size - 2;
+		kmerFilterLength = kmer_bit_size;
+		intWordFilter = 0;
+		charWordFilter = 0;
+		return;
+	} else {
+		longWordFilter = (((uint32_t) 1) << kmer_bit_size) - 1;	
+		kmerFilterIndex = LONGS;
+		kmerFilterOffset = kmer_bit_size - 2;
+		kmerFilterLength = kmer_bit_size;
+		intWordFilter = 0;
+		charWordFilter = 0;
+		return;
+	}
+#endif
+#if KMER_INTS
+	if (kmer_bit_size > 16)
+		kmer_bit_size -= 16;
+	else if (kmer_bit_size == 16) {
+		kmerFilterIndex = INTS;
+		kmerFilterOffset = kmer_bit_size - 2;
+		kmerFilterLength = kmer_bit_size;
+		charWordFilter = 0;
+		return;
+	} else {
+		intWordFilter = (((uint16_t) 1) << kmer_bit_size) - 1;	
+		kmerFilterIndex = INTS;
+		kmerFilterOffset = kmer_bit_size - 2;
+		kmerFilterLength = kmer_bit_size;
+		charWordFilter = 0;
+		return;
+	}
+
+#endif
+#if KMER_CHARS
+	if (kmer_bit_size < 8) 
+		charWordFilter = (((uint8_t) 1) << kmer_bit_size) - 1;	
+
+	kmerFilterIndex = CHARS;
+	kmerFilterOffset = kmer_bit_size - 2;
+	kmerFilterLength = kmer_bit_size;
+#endif
+
+}
+
+void resetKeyFilter(int keyLength) {
+	int kmer_bit_size = keyLength;
+
+	if (keyLength > MAXKMERLENGTH) 
+		exitErrorf(EXIT_FAILURE, true, "Key length %i greater than max allowed value (%i).\nRecompile Velvet to deal with this word length.", keyLength, MAXKMERLENGTH);
+
+#if KMER_CHARS
+	if (kmerFilterIndex == CHARS) {
+		if (kmer_bit_size > kmerFilterLength) {
+			kmer_bit_size -= kmerFilterLength;
+		} else {
+			keyFilterIndex = CHARS;
+			keyFilterLength = kmer_bit_size;
+			keyFilterOffset = kmerFilterLength - keyFilterLength;
+			keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;	
+			return;
+		}
+	}
+#endif
+#if KMER_INTS
+	if (kmerFilterIndex == INTS) {
+		if (kmer_bit_size > kmerFilterLength) {
+			kmer_bit_size -= kmerFilterLength;
+		} else {
+			keyFilterIndex = INTS;
+			keyFilterLength = kmer_bit_size;
+			keyFilterOffset = kmerFilterLength - keyFilterLength;
+			keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;	
+			return;
+		}
+	} else if (intWordFilter) {
+		if (kmer_bit_size > 16)
+			kmer_bit_size -= 16;
+		else {
+			keyFilterIndex = INTS;
+			keyFilterLength = kmer_bit_size;
+			keyFilterOffset = 16 - keyFilterLength;
+			keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;	
+			return;
+		}
+	}
+#endif
+#if KMER_LONGS
+	if (kmerFilterIndex == LONGS) {
+		if (kmer_bit_size > kmerFilterLength) {
+			kmer_bit_size -= kmerFilterLength;
+		} else {
+			keyFilterIndex = LONGS;
+			keyFilterLength = kmer_bit_size;
+			keyFilterOffset = kmerFilterLength - keyFilterLength;
+			keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;	
+			return;
+		}
+	} else if (longWordFilter) {
+		if (kmer_bit_size > 32)
+			kmer_bit_size -= 32;
+		else {
+			keyFilterIndex = LONGS;
+			keyFilterLength = kmer_bit_size;
+			keyFilterOffset = 32 - keyFilterLength;
+			keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;	
+			return;
+		}
+	}
+#endif
+#if KMER_LONGLONGS
+	if (kmerFilterIndex == LONGLONGS) {
+		if (kmer_bit_size > kmerFilterLength) {
+			kmer_bit_size -= kmerFilterLength;
+		} else {
+			keyFilterIndex = LONGLONGS;
+			longLongKeyFilterIndex = longLongKmerFilterIndex;
+			keyFilterLength = kmer_bit_size;
+			keyFilterOffset = kmerFilterLength - keyFilterLength;
+			keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;	
+			return;
+		}
+	} else {
+		if (kmer_bit_size > 64)
+			abort();
+		else {
+			keyFilterIndex = LONGLONGS;
+			longLongKeyFilterIndex = longLongKmerFilterIndex;
+			keyFilterLength = kmer_bit_size;
+			keyFilterOffset = 64 - keyFilterLength;
+			keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;	
+			return;
+		}
+	} 
+
+	if (kmer_bit_size > 64)
+		abort();
+	else {
+		keyFilterIndex = LONGLONGS;
+		longLongKeyFilterIndex = longLongKmerFilterIndex - 1;
+		keyFilterLength = kmer_bit_size;
+		keyFilterOffset = 64 - keyFilterLength;
+		keyFilter = ((((uint64_t) 1) << keyFilterLength) - 1) << keyFilterOffset;	
+		return;
+	}
+#endif
+
+}
+
+static void shiftRight(Kmer * kmer) {
+	uint64_t leftBits = 0;
+	uint64_t rightBits;
+
+#if KMER_CHARS
+
+#if KMER_INTS | KMER_LONGS | KMER_LONGLONGS
+	rightBits = kmer->chars & 3;
+#endif 
+
+	kmer->chars >>= 2;
+	kmer->chars += (uint8_t) leftBits;
+
+#if KMER_INTS | KMER_LONGS | KMER_LONGLONGS
+	leftBits = rightBits;
+#endif 
+#endif
+
+#if KMER_INTS
+
+#if KMER_LONGS | KMER_LONGLONGS
+	rightBits = kmer->ints & 3;
+#endif
+
+	leftBits <<= 14;
+	kmer->ints >>= 2;
+	kmer->ints += (uint16_t) leftBits;
+
+#if KMER_LONGS | KMER_LONGLONGS
+	leftBits = rightBits;
+#endif
+#endif
+
+#if KMER_LONGS
+
+#if KMER_LONGLONGS
+	rightBits = kmer->longs & 3;
+#endif
+
+	leftBits <<= 30;
+	kmer->longs >>= 2;
+	kmer->longs += (uint32_t) leftBits;
+
+#if KMER_LONGLONGS
+	leftBits = rightBits;
+#endif
+#endif 
+
+#if KMER_LONGLONGS
+	int i;
+	for (i = KMER_LONGLONGS - 1; i >= 0; i--) {
+		rightBits = kmer->longlongs[i] & 3;
+		leftBits <<= 62;
+		kmer->longlongs[i] >>= 2;
+		kmer->longlongs[i] += leftBits;
+		leftBits = rightBits;
+	}
+#endif
+}
+
+void copyKmers(Kmer* k1, Kmer* k2) {
+
+#if KMER_LONGLONGS
+	int i;
+	for (i = 0; i < KMER_LONGLONGS; i++)
+		k1->longlongs[i] = k2->longlongs[i];
+#endif
+#if KMER_LONGS
+	k1->longs = k2->longs;
+#endif
+#if KMER_INTS
+	k1->ints = k2->ints;
+#endif
+#if KMER_CHARS
+	k1->chars = k2->chars;
+#endif
+}
+
+int compareKmers(Kmer* k1, Kmer* k2) {
+#if KMER_LONGLONGS
+	int i;
+#endif
+
+#if KMER_CHARS
+	if (k1->chars == k2->chars)
+		;
+	else if (k1->chars > k2->chars)
+		return 1;
+	else 
+		return -1;
+#endif
+#if KMER_INTS
+	if (k1->ints == k2->ints)
+		;
+	else if (k1->ints > k2->ints)
+		return 1;
+	else 
+		return -1;
+#endif
+#if KMER_LONGS
+	if (k1->longs == k2->longs)
+		;
+	else if (k1->longs > k2->longs)
+		return 1;
+	else 
+		return -1;
+#endif
+#if KMER_LONGLONGS
+	for (i = KMER_LONGLONGS - 1; i >= 0; i--) {
+		if (k1->longlongs[i] == k2->longlongs[i])
+			continue;
+		else if (k1->longlongs[i] > k2->longlongs[i])
+			return 1;
+		else 
+			return -1;
+	}
+#endif
+
+	return 0;
+}
+
+void clearKmer(Kmer * kmer) {
+#if KMER_LONGLONGS
+	int i;
+	for (i = 0; i < KMER_LONGLONGS; i++)
+		kmer->longlongs[i] = 0;
+#endif
+#if KMER_LONGS
+	kmer->longs = 0;
+#endif
+#if KMER_INTS
+	kmer->ints = 0;
+#endif
+#if KMER_CHARS
+	kmer->chars = 0;
+#endif
+}
+
+void printKmer(Kmer * kmer) {
+
+#if KMER_CHARS
+	velvetLog("%hx\t", kmer->chars);
+#endif
+#if KMER_INTS
+	velvetLog("%x\t", kmer->ints);
+#endif
+#if KMER_LONGS
+	velvetLog("%x\t", kmer->longs);
+#endif
+#if KMER_LONGLONGS
+	int i;
+	for (i = KMER_LONGLONGS - 1; i >= 0; i--)
+		velvetLog("%llx\t", (long long) kmer->longlongs[i]);
+#endif
+	velvetLog("\n");
+}
+
+void pushNucleotide(Kmer * kmer, Nucleotide nucleotide) {
+
+#if KMER_LONGLONGS
+	uint64_t * ptr;
+	int i;
+#endif
+#if KMER_LONGLONGS > 1 | KMER_LONGS | KMER_INTS | KMER_CHARS
+	uint64_t leftBits; 
+#endif
+	uint64_t rightBits = 0;
+
+#if KMER_LONGLONGS
+	ptr = kmer->longlongs;
+
+#if KMER_LONGLONGS > 1
+	for (i = 0; i < longLongKmerFilterIndex; i++) {
+		leftBits = (*ptr & longLongLeftFilter);
+		leftBits >>= 62;
+		*ptr <<= 2;
+		*ptr += rightBits;
+		*ptr &= longLongWordFilter;
+		rightBits = leftBits;
+		ptr++;
+	}
+#endif
+
+#if KMER_LONGS | KMER_INTS | KMER_CHARS
+	leftBits = (*ptr & longLongLeftFilter);
+	leftBits >>= 62;
+#endif
+
+	*ptr <<= 2;
+	*ptr += rightBits;
+	*ptr &= longLongKmerFilter;
+
+#if KMER_LONGS | KMER_INTS | KMER_CHARS
+	rightBits = leftBits;
+#endif
+#endif
+
+#if KMER_LONGS
+
+#if KMER_INTS | KMER_CHARS
+	leftBits = kmer->longs & longLeftFilter;
+	leftBits >>= 30;
+#endif
+	kmer->longs <<= 2;
+	kmer->longs += rightBits;
+	kmer->longs &= longWordFilter;
+
+#if KMER_INTS | KMER_CHARS
+	rightBits = leftBits;
+#endif
+
+#endif
+
+#if KMER_INTS
+
+#if KMER_CHARS
+	leftBits = kmer->ints & intLeftFilter;
+	leftBits >>= 14;
+#endif 
+	kmer->ints <<= 2;
+	kmer->ints += rightBits;
+	kmer->ints &= intWordFilter;
+
+#if KMER_CHARS
+	rightBits = leftBits;
+#endif 
+
+#endif
+
+#if KMER_CHARS
+	kmer->chars <<= 2;
+	kmer->chars += rightBits;
+	kmer->chars &= charWordFilter;
+#endif
+
+#if KMER_LONGLONGS
+	kmer->longlongs[0] += nucleotide;
+	if (kmer->longlongs[0] >= nucleotide)
+		return;
+
+	for (i = 1; i < KMER_LONGLONGS; i++)
+		if (++kmer->longlongs[i])
+			return;
+#if KMER_LONGS
+	if (++kmer->longs)
+		return;
+#endif
+#if KMER_INTS
+	if (++kmer->ints)
+		return;
+#endif
+#if KMER_CHARS
+	++kmer->chars;
+#endif
+
+#else
+
+#if KMER_LONGS
+	kmer->longs += nucleotide;
+	if (kmer->longs >= nucleotide)
+		return;
+#if KMER_INTS
+	if (++kmer->ints)
+		return;
+#endif
+#if KMER_CHARS
+	++kmer->chars;
+#endif
+
+#else
+
+#if KMER_INTS
+	kmer->ints += nucleotide;
+	if (kmer->ints >= nucleotide)
+		return;
+#if KMER_CHARS
+	++kmer->chars;
+#endif
+
+#else 
+
+#if KMER_CHARS
+	kmer->chars += nucleotide;
+#endif
+
+#endif
+#endif
+#endif
+}
+
+Nucleotide popNucleotide(Kmer * kmer) {
+	Nucleotide nucl;
+
+#if KMER_LONGLONGS
+	nucl = kmer->longlongs[0] & 3;
+#elif KMER_LONGS
+	nucl = kmer->longs & 3;
+#elif KMER_INTS
+	nucl = kmer->ints & 3;
+#elif KMER_CHARS
+	nucl = kmer->chars & 3;
+#endif
+
+	shiftRight(kmer);
+	return nucl;
+}
+
+void reversePushNucleotide(Kmer * kmer, Nucleotide nucleotide) {
+	uint64_t templongLong = nucleotide;
+
+	shiftRight(kmer);
+
+	switch(kmerFilterIndex) {
+		case UNDEFINED:
+			abort();
+#if KMER_LONGLONGS
+		case LONGLONGS:
+			kmer->longlongs[longLongKmerFilterIndex] += templongLong << kmerFilterOffset; 			
+			return;
+#endif
+#if KMER_LONGS
+		case LONGS:
+			kmer->longs += templongLong << kmerFilterOffset; 			
+			return;
+#endif
+#if KMER_INTS
+		case INTS:
+			kmer->ints += templongLong << kmerFilterOffset; 			
+			return;
+#endif
+#if KMER_CHARS
+		case CHARS:
+			kmer->chars += templongLong << kmerFilterOffset; 			
+			return;
+#endif
+	}		
+
+	exitErrorf(EXIT_FAILURE, true, "Anomaly in k-mer filering");
+}
+
+KmerKey getKmerKey(Kmer * kmer) {
+	KmerKey key = 0;	
+
+#if KMER_CHARS
+	if (keyFilterIndex == CHARS) {
+		key = kmer->chars & keyFilter;
+		key >>= keyFilterOffset;
+		return key;
+	}
+#endif
+
+#if KMER_INTS
+	if (keyFilterIndex == INTS) {
+#if KMER_CHARS
+		key += kmer->chars;
+#endif
+		key <<= keyFilterLength;
+		key += (kmer->ints & keyFilter) >> keyFilterOffset;
+		return key;
+	}
+#endif
+
+#if KMER_LONGS
+	if (keyFilterIndex == LONGS) {
+#if KMER_CHARS
+		key += kmer->chars;
+#endif
+#if KMER_INTS
+		key <<= 16;
+		key += kmer->ints;
+#endif
+		key <<= keyFilterLength;
+		key += (kmer->longs & keyFilter) >> keyFilterOffset;
+		return key;
+	}
+#endif
+
+#if KMER_LONGLONGS
+	if (keyFilterIndex == LONGLONGS) {
+#if KMER_CHARS
+		key += kmer->chars;
+#endif
+#if KMER_INTS
+		key <<= 16;
+		key += kmer->ints;
+#endif
+#if KMER_LONGS
+		key <<= 32;
+		key += kmer->longs;
+#endif
+		if (longLongKeyFilterIndex != longLongKmerFilterIndex) {
+			key <<= kmerFilterLength;
+			key += kmer->longlongs[longLongKmerFilterIndex];
+		}
+		key <<= keyFilterLength;
+		key += (kmer->longlongs[longLongKeyFilterIndex] & keyFilter) >> keyFilterOffset;
+
+		return key;
+	}
+#endif
+	abort();
+	return 0;
+}