bio-velvet_underground 0.0.1

data/ext/src/src/allocArray.h

@@ -0,0 +1,86 @@
+/*
+Copyright 2009 Sylvain Foret (sylvain.foret@anu.edu.au) 
+
+    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 _ALLOC_ARRAY_H_
+#define _ALLOC_ARRAY_H_
+
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+
+#include "globals.h"
+
+typedef struct AllocArray_st AllocArray;
+typedef struct AllocArrayFreeElement_st AllocArrayFreeElement;
+
+struct AllocArray_st
+{
+	void **blocks;
+	AllocArrayFreeElement *freeElements;
+	size_t elementSize;
+	size_t blockSize;
+	size_t maxBlocks;
+	size_t currentBlocks;
+	size_t maxElements;
+	size_t currentElements;
+#ifdef DEBUG
+	char *name;
+	size_t elementsRecycled;
+	size_t elementsAllocated;
+#endif
+#ifdef _OPENMP
+	int nbThreads;
+#endif
+};
+
+AllocArray* newAllocArray (size_t elementSize, char *name);
+void destroyAllocArray (AllocArray *array);
+ArrayIdx allocArrayAllocate (AllocArray *array);
+void allocArrayFree (AllocArray *array, ArrayIdx idx);
+
+#define DECLARE_FAST_ACCESSORS(name, type, array) \
+/* Fast version, without null pointer checks */ \
+static inline type* name##_FI2P(ArrayIdx idx) \
+{ \
+	const ArrayIdx i = idx - 1; \
+	const ArrayIdx blockIdx = i / array->maxElements; \
+	const ArrayIdx elementIdx = i % array->maxElements; \
+	return &((type*)(array->blocks[blockIdx]))[elementIdx]; \
+} \
+/* Slower version, with null pointer checks */ \
+static inline type* name##_I2P(ArrayIdx idx) \
+{ \
+	if (idx != NULL_IDX) \
+		return name##_FI2P(idx); \
+	return NULL; \
+} 
+
+#ifdef _OPENMP
+// For multithreading: thread-specific alloc arrays 
+AllocArray *newAllocArrayArray(unsigned int n,
+			       size_t elementSize,
+			       char * name);
+void destroyAllocArrayArray(AllocArray * allocArray);
+ArrayIdx allocArrayArrayAllocate (AllocArray *array);
+void allocArrayArrayFree (AllocArray *array, ArrayIdx idx);
+#endif
+
+#endif /* _ALLOC_ARRAY_H_ */

data/ext/src/src/autoOpen.c

@@ -0,0 +1,107 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <sys/wait.h>
+#include <string.h>
+
+#include "autoOpen.h"
+
+// Implementation of "popen" that ignores stderr
+static FILE* popenNoStderr(const char *exe, const char *const argv[], int* retPid)
+{
+	int out[2];
+	int pid;
+	int rc;
+
+	rc = pipe(out);
+	if (rc<0)
+		goto error_out;
+
+	pid = fork();
+	if (pid > 0) { // parent
+		close(out[1]);
+                *retPid = pid;
+                return fdopen(out[0], "r");
+	} else if (pid == 0) { // child
+		close(out[0]);
+		close(1);
+		dup(out[1]);
+
+		close(0);   // Don't let child inherit stdin, nor stderr
+		close(2);
+
+		execvp(exe, (char**)argv);
+		exit(1);
+	} else
+		goto error_fork;
+
+	return NULL;
+
+error_fork:
+	close(out[0]);
+	close(out[1]);
+error_out:
+	return NULL;
+}
+
+static int pcloseNoStderr(int pid, FILE* out)
+{
+	int rc, status;
+        fclose(out);
+	rc = waitpid(pid, &status, 0);
+	return status;
+}
+
+
+static const char const* decompressors[] = {"","pigz", "gunzip", "pbunzip2", "bunzip2", NULL};
+
+AutoFile* openFileAuto(char*filename)
+{
+	AutoFile* seqFile = calloc(1, sizeof(AutoFile));
+  	int i;
+
+	if (strcmp(filename, "-")==0)
+		  exitErrorf(EXIT_FAILURE, false, "Cannot read from stdin in auto mode\n");
+
+	for (i=0; decompressors[i] ; i++) {
+		if (strlen(decompressors[i])==0) {
+			seqFile->file = fopen(filename, "r");
+			seqFile->pid = 0;
+			seqFile->decompressor = "Raw read";
+		} else {
+			//printf("Trying : %s\n", decompressors[i]);
+			char const* args[] = {decompressors[i], "-c", "-d", filename, NULL};
+			seqFile->file = popenNoStderr(args[0], args, &(seqFile->pid));
+			seqFile->decompressor = decompressors[i];
+		}
+
+		if (!seqFile->file)
+			continue;
+
+		int c = fgetc(seqFile->file);
+		if (c=='>' || c=='@') {
+			// Ok, looks like FASTA or FASTQ
+                	ungetc(c, seqFile->file);
+                        seqFile->first_char = c;
+			return seqFile;
+		} else {
+			if (seqFile->pid)
+				pcloseNoStderr(seqFile->pid, seqFile->file);
+			else
+				fclose(seqFile->file);
+		}
+	}
+	//printf("Unable to determine file type\n");
+	return NULL;
+}
+
+void closeFileAuto(AutoFile* seqFile)
+{
+	if (!seqFile)
+		return;
+
+	if (seqFile->pid)
+		pcloseNoStderr(seqFile->pid, seqFile->file);
+	else
+		fclose(seqFile->file);
+}

data/ext/src/src/autoOpen.h

@@ -0,0 +1,18 @@
+#ifndef AUTOOPEN_H_
+#define AUTOOPEN_H_
+
+#include "globals.h"
+#include "utility.h"
+
+typedef struct {
+	int pid;
+	FILE* file;
+	char const* decompressor;
+	int first_char;
+} AutoFile;
+
+AutoFile* openFileAuto(char*filename);
+
+void closeFileAuto(AutoFile* autoFile);
+
+#endif

data/ext/src/src/binarySequences.c

@@ -0,0 +1,813 @@
+/*
+Copyright 2011 Convey Computer Corporation (info@conveycomputer.com)
+
+    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 <string.h>
+#include <math.h>
+#include <time.h>
+#include <limits.h>
+
+#include "globals.h"
+#include "tightString.h"
+#include "readSet.h"
+#include "binarySequences.h"
+#include "utility.h"
+
+#if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+#include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
+#else
+#include "../third-party/zlib-1.2.3/zlib.h"
+#endif
+
+#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
+#  include <fcntl.h>
+#  include <io.h>
+#  define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
+#else
+#  define SET_BINARY_MODE(file)
+#endif
+
+// write defines, typedefs, and protos
+#define WRITE_BUF_SHFT		16	// byte shift and mask
+#define WRITE_BUF_SIZE		(1<<WRITE_BUF_SHFT)
+#define WRITE_BUF_MASK		(WRITE_BUF_SIZE-1)
+#define SHORT_NUCL_LENGTH	128	// Nucleotide length (2-bits each)
+
+void computeSecondInPair(ReadSet * reads);
+
+FILE *openCnySeqForRead(const char *fileName, CnyUnifiedSeqFileHeader *seqFileHeader)
+{
+	FILE *pFile;
+	if ((pFile = fopen(fileName, "rb")) == 0) {
+		velvetLog("Unable to open %s for reading\n", fileName);
+		return NULL;
+	}
+
+	if (fread(seqFileHeader, sizeof(*seqFileHeader), 1, pFile) != 1) {
+		velvetLog("Unable to read file %s\n", fileName);
+		fclose(pFile);
+		return NULL;
+	}
+
+	if (strncmp((char *)&seqFileHeader->m_magic, "CSQ0", 4) != 0) {
+		velvetLog("Unknown format for file %s\n", fileName);
+		fclose(pFile);
+		return NULL;
+	}
+
+	if (seqFileHeader->m_bFileWriteCompleted == false) {
+		velvetLog("Corrupted file, %s\n", fileName);
+		fclose(pFile);
+		return NULL;
+	}
+
+	if (seqFileHeader->m_numCategories > CATEGORIES) {
+		velvetLog("File %s has %d categories, please rebuild velvet to match\n", fileName, seqFileHeader->m_numCategories);
+		fclose(pFile);
+		return NULL;
+	}
+
+#ifdef COLOR
+	if (!seqFileHeader->m_bColor) {
+		velvetLog("File %s does not specify color, please rebuild velvet to match\n", fileName);
+		fclose(pFile);
+		return NULL;
+	}
+#else
+	if (seqFileHeader->m_bColor) {
+		velvetLog("File %s specifies color, please rebuild velvet to match\n", fileName);
+		fclose(pFile);
+		return NULL;
+	}
+#endif
+	return pFile;
+}
+
+static boolean refillCnySeqReadBuffer(SequencesReader *seqReadInfo) 
+{
+	uint64_t readLen = (USF_READ_BUF_SIZE < seqReadInfo->m_unifiedSeqFileHeader.m_seqNuclStoreSize - seqReadInfo->m_readBufPos) ?
+		USF_READ_BUF_SIZE : seqReadInfo->m_unifiedSeqFileHeader.m_seqNuclStoreSize - seqReadInfo->m_readBufPos;
+
+	if (readLen == 0)
+		return false;
+
+	if (fread(seqReadInfo->m_pReadBuffer, (uint32_t)readLen, 1, seqReadInfo->m_pFile) != 1) {
+		velvetLog("Unable to read file\n");
+		exit (1);
+	}
+
+	seqReadInfo->m_pCurrentReadPtr = seqReadInfo->m_pReadBuffer;
+	seqReadInfo->m_pReadBufEnd = seqReadInfo->m_pReadBuffer + readLen;
+	seqReadInfo->m_readBufPos += readLen;
+
+	if (seqReadInfo->m_pNextReadPtr >= seqReadInfo->m_pReadBufEnd) {
+		seqReadInfo->m_pNextReadPtr -= USF_READ_BUF_SIZE;
+	}
+
+	return true;
+}
+
+static int32_t readCnySeqUint8(SequencesReader *seqReadInfo)
+{
+	if (seqReadInfo->m_pCurrentReadPtr == seqReadInfo->m_pReadBufEnd && !refillCnySeqReadBuffer(seqReadInfo))
+	{
+		return -1;
+	}
+
+	// printf("m_pCurrentReadPtr %llx\n", (long long) pReadInfo->m_pCurrentReadPtr);
+	return *seqReadInfo->m_pCurrentReadPtr++;
+}
+
+uint32_t readCnySeqUint32(SequencesReader *seqReadInfo) 
+{
+	uint32_t data;
+	data = 0;
+	int i;
+	for (i = 0; i < 4; i += 1)
+		data |= readCnySeqUint8(seqReadInfo) << (i*8);
+	return data;
+}
+
+boolean advanceCnySeqCurrentRead(SequencesReader *seqReadInfo)
+{
+	// Perform consistency check, unused bits of previous sequence should have a fixed pattern
+	uint32_t finalNuclOffset = 1;
+	if (seqReadInfo->m_bIsRef) {
+		finalNuclOffset += (sizeof(seqReadInfo->m_refCnt));
+		finalNuclOffset += (sizeof(RefInfo) * seqReadInfo->m_refCnt);
+	}
+	if ((seqReadInfo->m_currentReadLength & 3) != 0 && ((seqReadInfo->m_pNextReadPtr - finalNuclOffset) >= seqReadInfo->m_pReadBuffer)) {
+		uint8_t mask = 0xFF << (seqReadInfo->m_currentReadLength & 3) * 2;
+		if ((*(seqReadInfo->m_pNextReadPtr - finalNuclOffset) & mask) != (0xAA & mask)) {
+			velvetLog("Cny seq consistency check failed in advance\n");
+#ifdef DEBUG
+			abort();
+#endif
+			exit(1);
+		}
+	}
+
+	seqReadInfo->m_pCurrentReadPtr = seqReadInfo->m_pNextReadPtr;
+	seqReadInfo->m_currentNuclReadIdx = 0;
+
+	// clear ref flag before each code check
+	seqReadInfo->m_bIsRef = false;
+	seqReadInfo->m_refCnt = 0;
+
+	for(;;) {
+		int32_t	code = readCnySeqUint8(seqReadInfo);
+		// printf("checking code %d\n", code);
+		switch (code & 0xc0) {
+			case 0x00:	// short sequence
+			case 0x40:
+				seqReadInfo->m_currentReadLength = code & 0x7f;
+				seqReadInfo->m_pNextReadPtr = seqReadInfo->m_pCurrentReadPtr + ((seqReadInfo->m_currentReadLength + 3) >> 2);
+				break;
+			case 0x80:	// long sequence
+				seqReadInfo->m_currentReadLength = readCnySeqUint32(seqReadInfo);
+				seqReadInfo->m_pNextReadPtr = seqReadInfo->m_pCurrentReadPtr + ((seqReadInfo->m_currentReadLength + 3) >> 2);
+				if (code & 0x20) {
+				    // ref info present
+				    seqReadInfo->m_bIsRef = true;
+				    seqReadInfo->m_pNextReadPtr += (sizeof(seqReadInfo->m_refCnt));
+				    // length is updated once count is read
+				}
+				break;
+			case 0xc0:	// new file / category
+				if (code == EOF) {
+					return false;
+				}
+				seqReadInfo->m_currCategory = (Category) readCnySeqUint32(seqReadInfo);
+				if (seqReadInfo->m_currCategory < 0 || seqReadInfo->m_currCategory > REFERENCE) {
+					velvetLog("Illegal category %d\n", (int32_t) seqReadInfo->m_currCategory);
+					exit(1);
+				}
+				continue;
+		}
+
+		if (seqReadInfo->m_currentReadLength > seqReadInfo->m_maxSeqLen ||
+				seqReadInfo->m_currentReadLength < seqReadInfo->m_minSeqLen) {
+			velvetLog("Cny seq consistency check failed, len mismatch\n");
+#ifdef DEBUG
+			abort();
+#endif
+			exit(1);
+		}
+
+		return true;
+
+	}
+}
+
+void resetCnySeqCurrentRead(SequencesReader *seqReadInfo) 
+{
+	seqReadInfo->m_pReadBufEnd = seqReadInfo->m_pReadBuffer;
+	seqReadInfo->m_pNextReadPtr = seqReadInfo->m_pReadBuffer;
+	seqReadInfo->m_pCurrentReadPtr = seqReadInfo->m_pReadBuffer;
+	seqReadInfo->m_currentReadLength = 0;
+	seqReadInfo->m_readBufPos = 0;
+
+	if (fseek(seqReadInfo->m_pFile, sizeof(CnyUnifiedSeqFileHeader), SEEK_SET) < 0) {
+		perror("Unable to seek\n");
+		exit(1);
+	}
+
+	advanceCnySeqCurrentRead(seqReadInfo);
+}
+
+void getCnySeqNucl(SequencesReader *seqReadInfo, uint8_t *sequence) {
+	uint32_t nuclIdx;
+	for (nuclIdx = 0; nuclIdx < seqReadInfo->m_currentReadLength; nuclIdx += 4) {
+		sequence[nuclIdx / 4] = (uint8_t)readCnySeqUint8(seqReadInfo);
+	}
+}
+
+ReadSet *importCnyReadSet(char *filename)
+{
+	IDnum sequenceCount, sequenceIndex;
+	ReadSet *reads;
+	uint8_t *tmp;
+	Coordinate totalLength = 0;
+	int arrayLength;
+	SequencesReader seqReadInfo;
+	memset(&seqReadInfo, 0, sizeof(seqReadInfo));
+
+	seqReadInfo.m_pFile = openCnySeqForRead(filename, &seqReadInfo.m_unifiedSeqFileHeader);
+	seqReadInfo.m_numCategories = seqReadInfo.m_unifiedSeqFileHeader.m_numCategories;
+	seqReadInfo.m_minSeqLen = seqReadInfo.m_unifiedSeqFileHeader.m_minSeqLen;
+	seqReadInfo.m_maxSeqLen = seqReadInfo.m_unifiedSeqFileHeader.m_maxSeqLen;
+	seqReadInfo.m_bIsRef = false;
+
+	if (seqReadInfo.m_pFile != NULL)
+		velvetLog("Reading CNY read set file %s\n", filename);
+	else
+		exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
+
+//	readInfo.m_pReadBuffer = mallocOrExit(USF_READ_BUF_SIZE, sizeof(*readInfo.m_pReadBuffer));
+	seqReadInfo.m_pReadBuffer = mallocOrExit(USF_READ_BUF_SIZE, uint8_t );
+	seqReadInfo.m_pCurrentReadPtr = seqReadInfo.m_pReadBufEnd = 0;
+
+	reads = newReadSet();
+
+	resetCnySeqCurrentRead(&seqReadInfo);
+	sequenceCount = seqReadInfo.m_unifiedSeqFileHeader.m_sequenceCnt;
+
+	velvetLog("%li sequences found\n", (long) sequenceCount);
+
+	reads->readCount = sequenceCount;
+
+	if (reads->readCount == 0) {
+		reads->sequences = NULL;
+		reads->categories = NULL;
+		free(seqReadInfo.m_pReadBuffer);
+		return reads;	
+	}
+
+	reads->sequences = NULL;
+	reads->categories = callocOrExit(sequenceCount, Category);
+	reads->tSequences = mallocOrExit(sequenceCount, TightString);
+	// note there is some overhead with the seq store
+	reads->tSeqMem = callocOrExit (seqReadInfo.m_unifiedSeqFileHeader.m_seqNuclStoreSize, char);
+	tmp = (uint8_t *) reads->tSeqMem;
+	uint8_t * arrayEnd = tmp + seqReadInfo.m_unifiedSeqFileHeader.m_seqNuclStoreSize;
+	// read all sequence and category info in one pass
+	for (sequenceIndex = 0; sequenceIndex < sequenceCount; sequenceIndex += 1) {
+		reads->categories[sequenceIndex] = seqReadInfo.m_currCategory;
+		if (sizeof(ShortLength) == sizeof(int16_t) && seqReadInfo.m_currentReadLength > SHRT_MAX) {
+			velvetLog("Read %li of length %lli, longer than limit %i\n",
+					(long) sequenceIndex + 1, (long long) seqReadInfo.m_currentReadLength, SHRT_MAX);
+			velvetLog("You should recompile Velvet with the LONGSEQUENCES option.\n");
+			exit(1);
+		}
+		// only use tString to reduce memory use
+		reads->tSequences[sequenceIndex].length = seqReadInfo.m_currentReadLength;
+		arrayLength = (reads->tSequences[sequenceIndex].length + 3) / 4;
+		if ((tmp + arrayLength) > arrayEnd) {
+			velvetLog("array location 0x%lx for seq %ld beyond end 0x%lx\n", (uint64_t) tmp, (uint64_t) sequenceIndex, (uint64_t) arrayEnd);
+			exit(1);
+		}
+		totalLength += arrayLength;
+		reads->tSequences[sequenceIndex].sequence = tmp;
+		getCnySeqNucl(&seqReadInfo, tmp);
+		if (seqReadInfo.m_bIsRef) {
+			seqReadInfo.m_refCnt = readCnySeqUint32(&seqReadInfo);
+			// now the next ptr is advanced
+			seqReadInfo.m_pNextReadPtr += (sizeof(RefInfo) * seqReadInfo.m_refCnt);
+			RefInfo refElem;
+			uint32_t refIdx;
+			for (refIdx = 0; refIdx < seqReadInfo.m_refCnt; refIdx++) {
+				// not actually used so just read past refs
+				refElem.m_referenceID = readCnySeqUint32(&seqReadInfo);
+				refElem.m_pos = readCnySeqUint32(&seqReadInfo);
+			}
+		}
+		tmp += arrayLength;
+		if (sequenceIndex < sequenceCount) {
+			advanceCnySeqCurrentRead(&seqReadInfo);
+		}
+	}
+
+	fclose(seqReadInfo.m_pFile);
+	computeSecondInPair(reads);
+
+	free(seqReadInfo.m_pReadBuffer);
+	velvetLog("Done\n");
+	return reads;
+
+}
+
+// write routines
+#define ADENINE		0
+#define CYTOSINE	1
+#define GUANINE		2
+#define THYMINE		3
+#define INVALID         5
+
+static void cnySeqHostBufferFull(SequencesWriter *seqWriteInfo)
+{
+    // The current Host buffer is full
+    switch (seqWriteInfo->m_hostBuffersInUse) {
+	case 1:	// buf[0] is full, start using buf[1]
+	    seqWriteInfo->m_pHostBufPtr = seqWriteInfo->m_pWriteBuffer[1];
+	    seqWriteInfo->m_pHostBufPtrMax = seqWriteInfo->m_pHostBufPtr + WRITE_BUF_SIZE;
+	    seqWriteInfo->m_hostBufferFilePos[1] = seqWriteInfo->m_hostBufferFilePos[0] + WRITE_BUF_SIZE;
+	    seqWriteInfo->m_hostBuffersInUse = 2;
+	    break;
+	case 2: // buf[0] and buf[1] are full, start using buf[2]
+	    seqWriteInfo->m_pHostBufPtr = seqWriteInfo->m_pWriteBuffer[2];
+	    seqWriteInfo->m_pHostBufPtrMax = seqWriteInfo->m_pHostBufPtr + WRITE_BUF_SIZE;
+	    seqWriteInfo->m_hostBufferFilePos[2] = seqWriteInfo->m_hostBufferFilePos[1] + WRITE_BUF_SIZE;
+	    seqWriteInfo->m_hostBuffersInUse = 3;
+	    break;
+	case 3: // all three buffers are full, write out buf[2] and reuse
+	    if (fseek(seqWriteInfo->m_pFile, seqWriteInfo->m_hostBufferFilePos[2], SEEK_SET) < 0) {
+		velvetLog("Unable to seek in CnyUnifiedSeq\n");
+		exit(1);
+	    }
+
+	    if (fwrite(seqWriteInfo->m_pWriteBuffer[2], WRITE_BUF_SIZE, 1, seqWriteInfo->m_pFile) != 1) {
+		velvetLog("Unable to write CnyUnifiedSeq\n");
+		exit(1);
+	    }
+
+	    seqWriteInfo->m_pHostBufPtr = seqWriteInfo->m_pWriteBuffer[2];
+	    seqWriteInfo->m_pHostBufPtrMax = seqWriteInfo->m_pHostBufPtr + WRITE_BUF_SIZE;
+	    seqWriteInfo->m_hostBufferFilePos[2] = seqWriteInfo->m_hostBufferFilePos[2] + WRITE_BUF_SIZE;
+	    break;
+	default:
+	    velvetLog("Unknown CnySeq host buffer state %d\n", seqWriteInfo->m_hostBuffersInUse);
+	    exit(1);
+	    break;
+    }
+}
+
+static void moveCnySeqNucleotides(SequencesWriter *seqWriteInfo)
+{
+    // move nucleotides in buffer to allow a four byte length value
+    // the current sequence may span two buffers
+
+    uint64_t bufIdx = (seqWriteInfo->m_hostBuffersInUse == 2) ? (seqWriteInfo->m_pHostBufPtr - seqWriteInfo->m_pWriteBuffer[1] + WRITE_BUF_SIZE) : (seqWriteInfo->m_pHostBufPtr - seqWriteInfo->m_pWriteBuffer[0]);
+    if (bufIdx + 4 > 2 * WRITE_BUF_SIZE) {
+	velvetLog("CnySeq bufIdx %ld too large\n", bufIdx);
+	exit(1);
+    }
+
+    if (bufIdx + 4 >= WRITE_BUF_SIZE) {
+	// continue writing to buf[1]
+	seqWriteInfo->m_pHostBufPtr = seqWriteInfo->m_pWriteBuffer[1] + (bufIdx + 4 - WRITE_BUF_SIZE);
+	seqWriteInfo->m_pHostBufPtrMax = seqWriteInfo->m_pWriteBuffer[1] + WRITE_BUF_SIZE;
+	seqWriteInfo->m_hostBufferFilePos[1] = seqWriteInfo->m_hostBufferFilePos[0] + WRITE_BUF_SIZE;
+	seqWriteInfo->m_hostBuffersInUse = 2;
+    } else
+	seqWriteInfo->m_pHostBufPtr += 4;
+
+    seqWriteInfo->m_insertCurrentIndex += 16;
+
+    uint64_t cnt;
+    for (cnt = (seqWriteInfo->m_insertLength+3)>>2; cnt > 0; cnt -= 1) {
+	seqWriteInfo->m_pWriteBuffer[(bufIdx+4) >> WRITE_BUF_SHFT][(bufIdx+4) & WRITE_BUF_MASK] = seqWriteInfo->m_pWriteBuffer[bufIdx >> WRITE_BUF_SHFT][bufIdx & WRITE_BUF_MASK];
+	bufIdx -= 1;
+    }
+}
+
+static void writeCnySeqNucleotide(uint8_t nucleotide, SequencesWriter *seqWriteInfo)
+{
+    if (seqWriteInfo->m_insertLength == SHORT_NUCL_LENGTH-1) {
+	moveCnySeqNucleotides(seqWriteInfo);
+    }
+    if ((seqWriteInfo->m_insertCurrentIndex & 0x3) == 0)
+	*seqWriteInfo->m_pHostBufPtr = 0;
+
+    *seqWriteInfo->m_pHostBufPtr = *seqWriteInfo->m_pHostBufPtr | (nucleotide << ((seqWriteInfo->m_insertCurrentIndex & 0x3) * 2));
+
+    seqWriteInfo->m_insertLength += 1;
+    seqWriteInfo->m_insertCurrentIndex += 1;
+
+    if ((seqWriteInfo->m_insertCurrentIndex & 0x3) == 0) {
+	seqWriteInfo->m_pHostBufPtr += 1;
+
+	if (seqWriteInfo->m_pHostBufPtr == seqWriteInfo->m_pHostBufPtrMax)
+	    cnySeqHostBufferFull(seqWriteInfo);
+    }
+}
+
+void cnySeqInsertNucleotideString(const char *pReadBuf, SequencesWriter *seqWriteInfo) {
+    uint8_t		nucleotide;
+
+    static boolean bInit = false;
+    static uint8_t charMap[256];
+
+    if (!bInit) {
+	bInit = true;
+	// anything unusual defaults to A
+	memset(charMap, ADENINE, 256);
+	charMap[(int)'C'] = charMap[(int)'c'] = CYTOSINE;
+	charMap[(int)'G'] = charMap[(int)'g'] = GUANINE;
+	charMap[(int)'T'] = charMap[(int)'t'] = THYMINE;
+	charMap[(int)'\0'] = 4;
+    }
+
+    for (;;) {
+	nucleotide = charMap[(int)*pReadBuf];
+	if (nucleotide < 4) {
+	    writeCnySeqNucleotide(nucleotide, seqWriteInfo);
+	    pReadBuf += 1;
+	    continue;
+	} else if (nucleotide == 4) {
+	    return;
+	} else {
+	    velvetLog("CnySeq unexpected char %c (%d)\n", *pReadBuf, (int) *pReadBuf);
+	    exit(1);
+	}
+    }
+}
+
+SequencesWriter * openCnySeqForWrite(const char *unifiedSeqFileName)
+{
+    SequencesWriter *seqWriteInfo = callocOrExit(1, SequencesWriter);
+    seqWriteInfo->m_pWriteBuffer[0] = NULL;
+    seqWriteInfo->m_pWriteBuffer[1] = NULL;
+    seqWriteInfo->m_pWriteBuffer[2] = NULL;
+    char seqNamesFileName[5000];
+
+    strcpy(seqNamesFileName, unifiedSeqFileName);
+    strcat(seqNamesFileName, ".names");
+
+#ifdef COLOR
+    seqWriteInfo->m_unifiedSeqFileHeader.m_bColor = true;
+#else
+    seqWriteInfo->m_unifiedSeqFileHeader.m_bColor = false;
+#endif
+
+    if ((seqWriteInfo->m_pFile = fopen(unifiedSeqFileName, "wb")) == 0) {
+	velvetLog("Unable to open %s for writing\n", unifiedSeqFileName);
+	exit(1);
+    }
+
+    if ((seqWriteInfo->m_nameFile = fopen(seqNamesFileName, "w")) == 0) {
+        velvetLog("Unable to open %s for writing\n", seqNamesFileName);
+        exit(1);
+    }
+
+    memcpy(&seqWriteInfo->m_unifiedSeqFileHeader.m_magic, "CSQ0", 4);
+    seqWriteInfo->m_unifiedSeqFileHeader.m_timeStamp = time(0);
+    seqWriteInfo->m_unifiedSeqFileHeader.m_bFileWriteCompleted = false;
+
+    if (fwrite(&seqWriteInfo->m_unifiedSeqFileHeader, sizeof(CnyUnifiedSeqFileHeader), 1, seqWriteInfo->m_pFile) != 1) {
+	velvetLog("Unable to write file %s\n", unifiedSeqFileName);
+	exit(1);
+    }
+
+    seqWriteInfo->m_insertCurrentIndex = 0;
+    seqWriteInfo->m_pWriteBuffer[0] = mallocOrExit(WRITE_BUF_SIZE, uint8_t);
+    seqWriteInfo->m_pWriteBuffer[1] = mallocOrExit(WRITE_BUF_SIZE, uint8_t);
+    seqWriteInfo->m_pWriteBuffer[2] = mallocOrExit(WRITE_BUF_SIZE, uint8_t);
+
+    seqWriteInfo->m_hostBufferFilePos[0] = sizeof(CnyUnifiedSeqFileHeader);
+
+    seqWriteInfo->m_pHostBufPtr = seqWriteInfo->m_pWriteBuffer[0];
+    seqWriteInfo->m_pHostBufPtrMax = seqWriteInfo->m_pWriteBuffer[0] + WRITE_BUF_SIZE;
+    seqWriteInfo->m_hostBuffersInUse = 1;
+    seqWriteInfo->m_fileSegmentWriteIdx = 0;	// file segment currently being written
+    seqWriteInfo->m_unifiedSeqFileHeader.m_sequenceCnt = 0;
+    seqWriteInfo->m_unifiedSeqFileHeader.m_minSeqLen = ~0LL;
+    seqWriteInfo->m_unifiedSeqFileHeader.m_maxSeqLen = 0;
+    seqWriteInfo->m_unifiedSeqFileHeader.m_totalSeqLen = 0;
+    return seqWriteInfo;
+}
+
+static void alignCnySeqToNextByteBoundary(SequencesWriter *seqWriteInfo)
+{
+    if ((seqWriteInfo->m_insertCurrentIndex & 0x3) != 0)
+	seqWriteInfo->m_pHostBufPtr += 1;
+
+    seqWriteInfo->m_insertCurrentIndex = (seqWriteInfo->m_insertCurrentIndex + 3) & ~0x3LL;
+
+    if (seqWriteInfo->m_pHostBufPtr == seqWriteInfo->m_pHostBufPtrMax) {
+	cnySeqHostBufferFull(seqWriteInfo);
+    }
+}
+
+static void writeCnySeqUint8(uint8_t uint8, SequencesWriter *seqWriteInfo)
+{
+    *seqWriteInfo->m_pHostBufPtr++ = uint8;
+    seqWriteInfo->m_insertCurrentIndex += 4;
+
+    if (seqWriteInfo->m_pHostBufPtr == seqWriteInfo->m_pHostBufPtrMax) {
+	cnySeqHostBufferFull(seqWriteInfo);
+    }
+}
+
+static void writeCnySeqUint32(uint32_t uint32, SequencesWriter *seqWriteInfo)
+{
+    int i;
+    for (i = 0; i < 4; i += 1)
+	writeCnySeqUint8((uint8_t)(uint32 >> (i*8)), seqWriteInfo);
+}
+
+void inputCnySeqFileStart(Category category, SequencesWriter *seqWriteInfo)
+{
+    if (category > REFERENCE) {
+	velvetLog("Found category %d beyond max of %d\n", category, REFERENCE);
+	exit(1);
+    }
+
+    alignCnySeqToNextByteBoundary(seqWriteInfo);
+    writeCnySeqUint8(0xc0, seqWriteInfo);
+    writeCnySeqUint32(category, seqWriteInfo);
+}
+
+void cnySeqInsertStart(SequencesWriter *seqWriteInfo)
+{
+    seqWriteInfo->m_unifiedSeqFileHeader.m_sequenceCnt += 1;
+
+    alignCnySeqToNextByteBoundary(seqWriteInfo);
+
+    seqWriteInfo->m_insertLength = 0;
+    seqWriteInfo->m_pHostLengthBufPtr = seqWriteInfo->m_pHostBufPtr;
+    seqWriteInfo->m_pHostLengthBufPtrMax = seqWriteInfo->m_pHostBufPtrMax;
+    seqWriteInfo->m_pHostBufPtr += 1;
+    seqWriteInfo->m_insertLengthIndex = seqWriteInfo->m_insertCurrentIndex >> 2;	// byte index
+    seqWriteInfo->m_insertCurrentIndex += 4; // allow for single byte header
+    seqWriteInfo->m_insertStartIndex = seqWriteInfo->m_insertCurrentIndex;
+
+    if (seqWriteInfo->m_pHostBufPtr == seqWriteInfo->m_pHostBufPtrMax)
+    {
+	cnySeqHostBufferFull(seqWriteInfo);
+    }
+
+    seqWriteInfo->m_position = 0;
+    seqWriteInfo->m_openMask = false;
+}
+
+void cnySeqInsertSequenceName(const char *name, IDnum readID, SequencesWriter *seqWriteInfo, Category cat) {
+	if (fprintf(seqWriteInfo->m_nameFile, "%s\t%li\t%li\n", name, (long) readID, (long) cat) < 0) {
+		velvetLog("Unable to write in name file\n");
+		exit(1);
+	}
+}
+
+void cnySeqInsertReferenceMask(SequencesWriter *seqWriteInfo, Mask *referenceMask) {
+	Mask *tmp;
+	for (tmp = referenceMask; tmp; tmp = tmp->next) {
+		if (fprintf(seqWriteInfo->m_nameFile, "%li\t%li\n", (long) tmp->start, (long) tmp->finish) < 0) {
+			velvetLog("Unable to write ref in name file\n");
+			exit(1);
+		}
+	}
+}
+
+void cnySeqInsertEnd(SequencesWriter *seqWriteInfo)
+{
+    uint8_t *tmp;
+
+    // fill last few empty nucleotides with a fixed pattern for consistency checking
+    if ((seqWriteInfo->m_insertCurrentIndex & 0x3) != 0) {
+	*seqWriteInfo->m_pHostBufPtr |= 0xAA << ((seqWriteInfo->m_insertCurrentIndex & 0x3)*2);
+    }
+
+    // collect read length statistics
+    if (seqWriteInfo->m_unifiedSeqFileHeader.m_minSeqLen > seqWriteInfo->m_insertLength)
+	seqWriteInfo->m_unifiedSeqFileHeader.m_minSeqLen = seqWriteInfo->m_insertLength;
+    if (seqWriteInfo->m_unifiedSeqFileHeader.m_maxSeqLen < seqWriteInfo->m_insertLength)
+	seqWriteInfo->m_unifiedSeqFileHeader.m_maxSeqLen = seqWriteInfo->m_insertLength;
+
+    seqWriteInfo->m_unifiedSeqFileHeader.m_totalSeqLen += seqWriteInfo->m_insertLength;
+
+    if (seqWriteInfo->m_insertLength >= SHORT_NUCL_LENGTH || seqWriteInfo->m_bIsRef) {
+	if (seqWriteInfo->m_bIsRef) {
+	    alignCnySeqToNextByteBoundary(seqWriteInfo);
+
+	    if (seqWriteInfo->m_insertLength < SHORT_NUCL_LENGTH) {
+		    // the align above points to next byte,
+		    // need to back up to last byte of nucl seq
+		    seqWriteInfo->m_pHostBufPtr -= 1;
+		    moveCnySeqNucleotides(seqWriteInfo);
+		    // move to next byte
+		    seqWriteInfo->m_pHostBufPtr += 1;
+	    }
+
+	    // write out map info
+	    int idx;
+	    for (idx = 0; idx < 4; idx += 1) {
+		if (seqWriteInfo->m_pHostBufPtr == seqWriteInfo->m_pHostBufPtrMax)
+		    cnySeqHostBufferFull(seqWriteInfo);
+		*seqWriteInfo->m_pHostBufPtr++ = (seqWriteInfo->m_refCnt >> (idx*8)) & 0xff;
+		seqWriteInfo->m_insertCurrentIndex += 4; // single byte
+	    }
+	    int refIdx;
+	    RefInfoList *refElem = seqWriteInfo->m_refInfoHead;
+	    RefInfoList *prev = NULL;
+	    for (refIdx = 0; refIdx < seqWriteInfo->m_refCnt; refIdx++) {
+
+		    if (refElem == NULL) {
+			    velvetLog("reference but element %d NULL\n", refIdx);
+			    exit(1);
+		    }
+		    alignCnySeqToNextByteBoundary(seqWriteInfo);
+
+		    for (idx = 0; idx < 4; idx += 1) {
+			    if (seqWriteInfo->m_pHostBufPtr == seqWriteInfo->m_pHostBufPtrMax)
+				    cnySeqHostBufferFull(seqWriteInfo);
+			    *seqWriteInfo->m_pHostBufPtr++ = (refElem->m_elem.m_referenceID >> (idx*8)) & 0xff;
+			    seqWriteInfo->m_insertCurrentIndex += 4; // single byte
+		    }
+		    for (idx = 0; idx < 4; idx += 1) {
+			    if (seqWriteInfo->m_pHostBufPtr == seqWriteInfo->m_pHostBufPtrMax)
+				    cnySeqHostBufferFull(seqWriteInfo);
+			    *seqWriteInfo->m_pHostBufPtr++ = (refElem->m_elem.m_pos >> (idx*8)) & 0xff;
+			    seqWriteInfo->m_insertCurrentIndex += 4; // single byte
+		    }
+
+		    prev = refElem;
+		    refElem = refElem->next;
+		    free(prev);
+	    }
+	    if (refElem != NULL) {
+		    velvetLog("more than %d elements in ref\n", seqWriteInfo->m_refCnt);
+		    exit(1);
+	    }
+	    seqWriteInfo->m_bIsRef = false;
+	    seqWriteInfo->m_refInfoHead = NULL;
+	    seqWriteInfo->m_refCnt = 0;	    // set ref bit
+	    *(seqWriteInfo->m_pHostLengthBufPtr++) = 0xa0 | ((seqWriteInfo->m_insertLength >> 32) & 0x1f);
+	} else {
+	    // one byte control, four byte length
+	    *(seqWriteInfo->m_pHostLengthBufPtr++) = 0x80 | ((seqWriteInfo->m_insertLength >> 32) & 0x1f);
+	}
+	int idx;
+	for (idx = 0; idx < 4; idx += 1) {
+	    if (seqWriteInfo->m_pHostLengthBufPtr == seqWriteInfo->m_pHostLengthBufPtrMax) {
+		if (seqWriteInfo->m_hostBuffersInUse < 2) {
+		    velvetLog("CnySeq m_hostBuffersInUse %d\n", seqWriteInfo->m_hostBuffersInUse);
+		    exit(1);
+		}
+		seqWriteInfo->m_pHostLengthBufPtr = seqWriteInfo->m_pWriteBuffer[1];
+	    }
+	    *seqWriteInfo->m_pHostLengthBufPtr++ = (seqWriteInfo->m_insertLength >> (idx*8)) & 0xff;
+	}
+
+    } else {
+	// one byte length;
+	*seqWriteInfo->m_pHostLengthBufPtr = (uint8_t)seqWriteInfo->m_insertLength;
+    }
+
+    alignCnySeqToNextByteBoundary(seqWriteInfo);
+
+    switch (seqWriteInfo->m_hostBuffersInUse) {
+	case 1:	// buf[0] is being written
+	    break;
+	case 2: // buf[0] and buf[1] are being written, write buf[0] to disk
+	    if (fseek(seqWriteInfo->m_pFile, seqWriteInfo->m_hostBufferFilePos[0], SEEK_SET) < 0) {
+		velvetLog("Unable to seek in CnyUnifiedSeq\n");
+		exit(1);
+	    }
+
+	    if (fwrite(seqWriteInfo->m_pWriteBuffer[0], WRITE_BUF_SIZE, 1, seqWriteInfo->m_pFile) != 1) {
+		velvetLog("Unable to write CnyUnifiedSeq\n");
+		exit(1);
+	    }
+
+	    // swap buf[0] and buf[1]
+	    tmp = seqWriteInfo->m_pWriteBuffer[0];
+	    seqWriteInfo->m_pWriteBuffer[0] = seqWriteInfo->m_pWriteBuffer[1];
+	    seqWriteInfo->m_pWriteBuffer[1] = tmp;
+
+	    seqWriteInfo->m_hostBufferFilePos[0] = seqWriteInfo->m_hostBufferFilePos[1];
+
+	    seqWriteInfo->m_hostBuffersInUse = 1;
+	    break;
+	case 3: // buf[0], [1] and [2] are in use, write buf[0] and [1] to disk
+	    if (fseek(seqWriteInfo->m_pFile, seqWriteInfo->m_hostBufferFilePos[0], SEEK_SET) < 0) {
+		velvetLog("Unable to seek in CnyUnifiedSeq\n");
+		exit(1);
+	    }
+
+
+	    if (fwrite(seqWriteInfo->m_pWriteBuffer[0], WRITE_BUF_SIZE, 1, seqWriteInfo->m_pFile) != 1){
+		velvetLog("Unable to write CnyUnifiedSeq\n");
+		exit(1);
+	    }
+
+
+	    if (fseek(seqWriteInfo->m_pFile, seqWriteInfo->m_hostBufferFilePos[1], SEEK_SET) < 0) {
+		velvetLog("Unable to seek in CnyUnifiedSeq\n");
+		exit(1);
+	    }
+
+
+	    if (fwrite(seqWriteInfo->m_pWriteBuffer[1], WRITE_BUF_SIZE, 1, seqWriteInfo->m_pFile) != 1){
+		velvetLog("Unable to write CnyUnifiedSeq\n");
+		exit(1);
+	    }
+
+	    // swap buf[0] and buf[2]
+	    tmp = seqWriteInfo->m_pWriteBuffer[0];
+	    seqWriteInfo->m_pWriteBuffer[0] = seqWriteInfo->m_pWriteBuffer[2];
+	    seqWriteInfo->m_pWriteBuffer[2] = tmp;
+
+	    seqWriteInfo->m_hostBufferFilePos[0] = seqWriteInfo->m_hostBufferFilePos[2];
+
+	    seqWriteInfo->m_hostBuffersInUse = 1;
+	    break;
+    }
+
+    // if ref masks, write mapping info to the names file
+    if (seqWriteInfo->m_referenceMask && *(seqWriteInfo->m_referenceMask)) {
+	    cnySeqInsertReferenceMask(seqWriteInfo, *(seqWriteInfo->m_referenceMask));
+	    // free memory and clear list
+	    if (seqWriteInfo->m_maskMemory) {
+		    destroyRecycleBin(seqWriteInfo->m_maskMemory);
+		    seqWriteInfo->m_maskMemory = NULL;
+	    }
+	    *(seqWriteInfo->m_referenceMask) = NULL;
+    }
+}
+
+void closeCnySeqForWrite(SequencesWriter *seqWriteInfo)
+{
+    // should be only one buffer in use
+    if (seqWriteInfo->m_hostBuffersInUse != 1) {
+	velvetLog("CnySeq host buffers in use %d\n", seqWriteInfo->m_hostBuffersInUse);
+	exit(1);
+    }
+
+    if (fseek(seqWriteInfo->m_pFile, seqWriteInfo->m_hostBufferFilePos[0], SEEK_SET) < 0) {
+	velvetLog("Unable to seek CnySeq\n");
+	exit(1);
+    }
+
+    if (fwrite(seqWriteInfo->m_pWriteBuffer[0], (uint32_t)(seqWriteInfo->m_pHostBufPtr - seqWriteInfo->m_pWriteBuffer[0]), 1, seqWriteInfo->m_pFile) != 1) {
+	velvetLog("Unable to write CnySeq\n");
+	exit(1);
+    }
+
+    seqWriteInfo->m_unifiedSeqFileHeader.m_bFileWriteCompleted = true;
+    seqWriteInfo->m_unifiedSeqFileHeader.m_seqNuclStoreSize = seqWriteInfo->m_insertCurrentIndex >> 2;
+    seqWriteInfo->m_unifiedSeqFileHeader.m_numCategories = CATEGORIES;
+
+    if (fseek(seqWriteInfo->m_pFile, 0, SEEK_SET) < 0) {
+	velvetLog("Unable to seek CnySeq\n");
+	exit(1);
+    }
+
+    if (fwrite(&seqWriteInfo->m_unifiedSeqFileHeader, sizeof(CnyUnifiedSeqFileHeader), 1, seqWriteInfo->m_pFile) != 1) {
+	velvetLog("Unable to write CnySeq\n");
+	exit(1);
+    }
+
+    if (fclose(seqWriteInfo->m_pFile) < 0) {
+	velvetLog("Unable to close CnySeq\n");
+	exit(1);
+    }
+
+    if (fclose(seqWriteInfo->m_nameFile) < 0) {
+	velvetLog("Unable to close names file\n");
+	exit(1);
+    }
+
+    if (seqWriteInfo->m_pWriteBuffer[0])
+        free(seqWriteInfo->m_pWriteBuffer[0]);
+    if (seqWriteInfo->m_pWriteBuffer[1])
+        free(seqWriteInfo->m_pWriteBuffer[1]);
+    if (seqWriteInfo->m_pWriteBuffer[2])
+        free(seqWriteInfo->m_pWriteBuffer[2]);
+}