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 +1,30 @@
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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 _READCOHERENTGRAPH_H_
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#define _READCOHERENTGRAPH_H_
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void readCoherentGraph(Graph * graph, boolean(*isUnique) (Node * node),
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double coverage, ReadSet * reads);
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boolean isUniqueSolexa(Node * node);
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void setMultiplicityCutoff(int value);
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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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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 <string.h>
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#include <math.h>
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#include <time.h>
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#include <limits.h>
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#include <ctype.h>
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#include "globals.h"
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#include "tightString.h"
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#include "readSet.h"
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#include "utility.h"
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#include "binarySequences.h"
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#include "autoOpen.h"
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#include "kseq.h"
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#if !defined(BUNDLEDZLIB)
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#include <zlib.h>
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#elif defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
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#include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
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#else
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#include "../third-party/zlib-1.2.3/zlib.h"
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#endif
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#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
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# include <fcntl.h>
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# include <io.h>
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# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
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#else
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# define SET_BINARY_MODE(file)
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#endif
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static Mask *allocateMask(SequencesWriter *seqWriteInfo)
|
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{
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if (seqWriteInfo->m_maskMemory == NULL)
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seqWriteInfo->m_maskMemory = newRecycleBin(sizeof(Mask), 10000);
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return (Mask *) allocatePointer(seqWriteInfo->m_maskMemory);
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}
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static Mask * newMask(SequencesWriter *seqWriteInfo, Coordinate position)
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{
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Mask * mask = allocateMask(seqWriteInfo);
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mask->start = position;
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mask->finish = position;
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mask->next = NULL;
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return mask;
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}
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//
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// cmd line args can override the createBinary flag
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// note that createBinary is only used by velveth
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//
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boolean createBinary = false;
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boolean isCreateBinary()
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{
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return createBinary;
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}
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void setCreateBinary(boolean val)
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{
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createBinary = val;
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}
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ReadSet *newReadSet()
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{
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ReadSet *rs = callocOrExit(1, ReadSet);
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return rs;
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}
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//////////////////////////////////////////////////////////////////////////
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// Reference identifiers
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//////////////////////////////////////////////////////////////////////////
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typedef struct referenceCoordinate_st ReferenceCoordinate;
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static Coordinate reference_coordinate_double_strand = true;
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struct referenceCoordinate_st {
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char * name;
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Coordinate start;
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Coordinate finish;
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IDnum referenceID;
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IDnum counter;
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boolean positive_strand;
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} ATTRIBUTE_PACKED;
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static int compareRefCoords(const void * ptrA, const void * ptrB) {
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ReferenceCoordinate * A = (ReferenceCoordinate *) ptrA;
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ReferenceCoordinate * B = (ReferenceCoordinate *) ptrB;
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int comp = strcmp(A->name, B->name);
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if (comp != 0)
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return comp;
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else if (!reference_coordinate_double_strand && A->positive_strand != B->positive_strand)
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return A->positive_strand > B->positive_strand;
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else {
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if (A->finish > -1 && A->finish < B->start)
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return -1;
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else if (B->finish > -1 && A->start > B->finish)
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return 1;
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else return 0;
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}
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}
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typedef struct referenceCoordinateTable_st ReferenceCoordinateTable;
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struct referenceCoordinateTable_st {
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ReferenceCoordinate * array;
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IDnum arrayLength;
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} ATTRIBUTE_PACKED;
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static ReferenceCoordinateTable * newReferenceCoordinateTable() {
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ReferenceCoordinateTable * table = callocOrExit(1, ReferenceCoordinateTable);
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table->array = NULL;
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table->arrayLength = 0;
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return table;
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}
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static void printReferenceCoordinateTableStats(ReferenceCoordinateTable * table) {
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IDnum index;
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IDnum counter = 0;
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velvetLog("Reference mapping counters\n");
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velvetLog("Name\tRead mappings\n");
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for (index = 0; index < table->arrayLength; index++) {
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velvetLog("%s\t%li\n", table->array[index].name, (long) table->array[index].counter);
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counter += table->array[index].counter;
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}
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if (counter == 0) {
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velvetLog("WARNING: None of your read mappings recognized the reference sequence!\n");
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velvetLog("Double check that the names are identical between reference fasta headers and SAM/BAM sequences.\n");
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}
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}
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static void destroyReferenceCoordinateTable(ReferenceCoordinateTable * table) {
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IDnum index;
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159
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if (table->array) {
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printReferenceCoordinateTableStats(table);
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for (index = 0; index < table->arrayLength; index++)
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free(table->array[index].name);
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free(table->array);
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165
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}
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free(table);
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167
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}
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168
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static void resizeReferenceCoordinateTable(ReferenceCoordinateTable * table, IDnum extraLength) {
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if (table->array == NULL)
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table->array = callocOrExit(extraLength, ReferenceCoordinate);
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else
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table->array = reallocOrExit(table->array, table->arrayLength + extraLength, ReferenceCoordinate);
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}
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static ReferenceCoordinate * findReferenceCoordinate(ReferenceCoordinateTable * table, char * name, Coordinate start, Coordinate finish, boolean positive_strand) {
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ReferenceCoordinate * array = table->array;
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ReferenceCoordinate refCoord;
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179
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Coordinate leftIndex = 0;
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Coordinate rightIndex = table->arrayLength - 1;
|
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Coordinate middleIndex;
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182
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refCoord.name = name;
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refCoord.start = start;
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refCoord.finish = finish;
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refCoord.referenceID = 0;
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187
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refCoord.positive_strand = positive_strand;
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188
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189
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while (true) {
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190
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middleIndex = (rightIndex + leftIndex) / 2;
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|
192
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if (leftIndex > rightIndex)
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return NULL;
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194
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else if (compareRefCoords(&(array[middleIndex]), &refCoord) == 0)
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195
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return &(array[middleIndex]);
|
196
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else if (leftIndex == middleIndex)
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197
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return NULL;
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198
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else if (compareRefCoords(&(array[middleIndex]), &refCoord) > 0)
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199
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rightIndex = middleIndex;
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200
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else
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201
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leftIndex = middleIndex;
|
202
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}
|
203
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}
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204
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|
205
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static void addReferenceCoordinate(ReferenceCoordinateTable * table, char * name, Coordinate start, Coordinate finish, boolean positive_strand) {
|
206
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ReferenceCoordinate * refCoord;
|
207
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|
208
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if ((refCoord = findReferenceCoordinate(table, name, start, finish, positive_strand))) {
|
209
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velvetLog("Overlapping reference coordinates:\n");
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210
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velvetLog("%s:%lli-%lli\n", name, (long long) start, (long long) finish);
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211
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+
velvetLog("%s:%lli-%lli\n", refCoord->name, (long long) refCoord->start, (long long) refCoord->finish);
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212
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velvetLog("Exiting...\n");
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213
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#ifdef DEBUG
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214
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abort();
|
215
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+
#endif
|
216
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+
exit(1);
|
217
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+
}
|
218
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+
|
219
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+
refCoord = &(table->array[table->arrayLength++]);
|
220
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+
|
221
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refCoord->name = name;
|
222
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refCoord->start = start;
|
223
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refCoord->finish = finish;
|
224
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refCoord->referenceID = table->arrayLength;
|
225
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refCoord->positive_strand = positive_strand;
|
226
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refCoord->counter = 0;
|
227
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}
|
228
|
+
|
229
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static void sortReferenceCoordinateTable(ReferenceCoordinateTable * table) {
|
230
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qsort(table->array, table->arrayLength, sizeof(ReferenceCoordinate), compareRefCoords);
|
231
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+
}
|
232
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+
|
233
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+
//////////////////////////////////////////////////////////////////////////
|
234
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// File reading
|
235
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+
//////////////////////////////////////////////////////////////////////////
|
236
|
+
|
237
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+
static void velvetifySequence(char * str, SequencesWriter *seqWriteInfo) {
|
238
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+
int i;
|
239
|
+
char c;
|
240
|
+
size_t length = strlen(str);
|
241
|
+
|
242
|
+
for (i = 0; i < length; i++) {
|
243
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+
c = str[i];
|
244
|
+
switch (c) {
|
245
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+
case '\n':
|
246
|
+
case '\r':
|
247
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+
case EOF:
|
248
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+
str[i] = '\0';
|
249
|
+
break;
|
250
|
+
case 'A':
|
251
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+
case 'a':
|
252
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+
str[i] = 'A';
|
253
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+
break;
|
254
|
+
case 'C':
|
255
|
+
case 'c':
|
256
|
+
str[i] = 'C';
|
257
|
+
break;
|
258
|
+
case 'G':
|
259
|
+
case 'g':
|
260
|
+
str[i] = 'G';
|
261
|
+
break;
|
262
|
+
case 'T':
|
263
|
+
case 't':
|
264
|
+
str[i] = 'T';
|
265
|
+
break;
|
266
|
+
default:
|
267
|
+
str[i] = 'N';
|
268
|
+
}
|
269
|
+
// non NULL indicates ref masks are being created
|
270
|
+
if (seqWriteInfo->m_referenceMask != NULL) {
|
271
|
+
if (str[i] == 'N') {
|
272
|
+
if (seqWriteInfo->m_openMask) {
|
273
|
+
seqWriteInfo->m_current->finish++;
|
274
|
+
} else if (*(seqWriteInfo->m_referenceMask) == NULL) {
|
275
|
+
*(seqWriteInfo->m_referenceMask) = newMask(seqWriteInfo, seqWriteInfo->m_position);
|
276
|
+
seqWriteInfo->m_current = *(seqWriteInfo->m_referenceMask);
|
277
|
+
} else {
|
278
|
+
seqWriteInfo->m_current->next = newMask(seqWriteInfo, seqWriteInfo->m_position);
|
279
|
+
seqWriteInfo->m_current = seqWriteInfo->m_current->next;
|
280
|
+
}
|
281
|
+
seqWriteInfo->m_openMask = true;
|
282
|
+
seqWriteInfo->m_position += 1;
|
283
|
+
} else if (str[i] != '\0') {
|
284
|
+
seqWriteInfo->m_openMask = false;
|
285
|
+
seqWriteInfo->m_position += 1;
|
286
|
+
}
|
287
|
+
}
|
288
|
+
}
|
289
|
+
}
|
290
|
+
|
291
|
+
static void reverseComplementSequence(char * str)
|
292
|
+
{
|
293
|
+
size_t length = strlen(str);
|
294
|
+
size_t i;
|
295
|
+
|
296
|
+
for (i = 0; i < length-1 - i; i++) {
|
297
|
+
char c = str[i];
|
298
|
+
str[i] = str[length-1 - i];
|
299
|
+
str[length-1 - i] = c;
|
300
|
+
}
|
301
|
+
|
302
|
+
#ifndef COLOR
|
303
|
+
for (i = 0; i < length; i++) {
|
304
|
+
switch (str[i]) {
|
305
|
+
case 'A':
|
306
|
+
case 'a':
|
307
|
+
str[i] = 'T';
|
308
|
+
break;
|
309
|
+
case 'C':
|
310
|
+
case 'c':
|
311
|
+
str[i] = 'G';
|
312
|
+
break;
|
313
|
+
case 'G':
|
314
|
+
case 'g':
|
315
|
+
str[i] = 'C';
|
316
|
+
break;
|
317
|
+
// As in velvetifySequence(), anything unusual ends up as 'A'
|
318
|
+
default:
|
319
|
+
str[i] = 'A';
|
320
|
+
break;
|
321
|
+
}
|
322
|
+
}
|
323
|
+
#endif
|
324
|
+
}
|
325
|
+
|
326
|
+
static void writeFastaSequence(FILE * outfile, const char * str)
|
327
|
+
{
|
328
|
+
size_t length = strlen(str);
|
329
|
+
size_t start;
|
330
|
+
for (start = 0; start < length; start += 60)
|
331
|
+
velvetFprintf(outfile, "%.60s\n", &str[start]);
|
332
|
+
}
|
333
|
+
|
334
|
+
void convertSequences(ReadSet * rs)
|
335
|
+
{
|
336
|
+
rs->tSequences = newTightStringArrayFromStringArray(rs->sequences,
|
337
|
+
rs->readCount,
|
338
|
+
&rs->tSeqMem);
|
339
|
+
rs->sequences = NULL;
|
340
|
+
}
|
341
|
+
|
342
|
+
// Returns the value of a 32-bit little-endian-stored integer.
|
343
|
+
static int int32(const unsigned char * ptr)
|
344
|
+
{
|
345
|
+
int x = ptr[3];
|
346
|
+
x = (x << 8) | ptr[2];
|
347
|
+
x = (x << 8) | ptr[1];
|
348
|
+
x = (x << 8) | ptr[0];
|
349
|
+
return x;
|
350
|
+
}
|
351
|
+
|
352
|
+
void goToEndOfLine(char *line, FILE * file)
|
353
|
+
{
|
354
|
+
size_t length = strlen(line);
|
355
|
+
char c = line[length - 1];
|
356
|
+
|
357
|
+
while (c != '\n')
|
358
|
+
c = fgetc(file);
|
359
|
+
}
|
360
|
+
|
361
|
+
static void writeSeqName(char*seq_name, SequencesWriter *seqWriteInfo, Category cat, IDnum *sequenceIndex)
|
362
|
+
{
|
363
|
+
char name[5001];
|
364
|
+
if (isCreateBinary()) {
|
365
|
+
cnySeqInsertStart(seqWriteInfo);
|
366
|
+
sprintf(name, ">%s", seq_name);
|
367
|
+
cnySeqInsertSequenceName(name, (long) ((*sequenceIndex)++), seqWriteInfo, cat);
|
368
|
+
} else {
|
369
|
+
velvetFprintf(seqWriteInfo->m_pFile,">%s\t%ld\t%d\n", seq_name, (long) ((*sequenceIndex)++), (int) cat);
|
370
|
+
}
|
371
|
+
}
|
372
|
+
|
373
|
+
static void writeSequence(char*seq, SequencesWriter *seqWriteInfo)
|
374
|
+
{
|
375
|
+
char str[100];
|
376
|
+
velvetifySequence(seq, seqWriteInfo);
|
377
|
+
if (isCreateBinary()) {
|
378
|
+
cnySeqInsertNucleotideString(seq, seqWriteInfo);
|
379
|
+
cnySeqInsertEnd(seqWriteInfo);
|
380
|
+
} else {
|
381
|
+
Coordinate start = 0;
|
382
|
+
while (start <= strlen(seq)) {
|
383
|
+
strncpy(str, seq + start, 60);
|
384
|
+
str[60] = '\0';
|
385
|
+
velvetFprintf(seqWriteInfo->m_pFile, "%s\n", str);
|
386
|
+
start += 60;
|
387
|
+
}
|
388
|
+
}
|
389
|
+
}
|
390
|
+
|
391
|
+
static void initFastX(SequencesWriter *seqWriteInfo, Category cat)
|
392
|
+
{
|
393
|
+
seqWriteInfo->m_referenceMask = NULL;
|
394
|
+
seqWriteInfo->m_position = 0;
|
395
|
+
seqWriteInfo->m_openMask = false;
|
396
|
+
|
397
|
+
// Binary file stuff
|
398
|
+
if (isCreateBinary() && (cat == REFERENCE)) {
|
399
|
+
seqWriteInfo->m_referenceMask = callocOrExit(1, Mask*);
|
400
|
+
}
|
401
|
+
if (isCreateBinary()) {
|
402
|
+
inputCnySeqFileStart(cat, seqWriteInfo);
|
403
|
+
}
|
404
|
+
}
|
405
|
+
|
406
|
+
static void cleanupFastX(SequencesWriter *seqWriteInfo, Category cat)
|
407
|
+
{
|
408
|
+
if (seqWriteInfo->m_referenceMask) {
|
409
|
+
free(seqWriteInfo->m_referenceMask);
|
410
|
+
seqWriteInfo->m_referenceMask = NULL;
|
411
|
+
}
|
412
|
+
}
|
413
|
+
|
414
|
+
|
415
|
+
// Imports sequences from a raw sequence file
|
416
|
+
// Memory space allocated within this function.
|
417
|
+
static void readRawFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum * sequenceIndex)
|
418
|
+
{
|
419
|
+
FILE *file;
|
420
|
+
const int maxline = 5000;
|
421
|
+
char line[5000];
|
422
|
+
IDnum counter = 0;
|
423
|
+
|
424
|
+
initFastX(seqWriteInfo, cat);
|
425
|
+
|
426
|
+
if (strcmp(filename, "-"))
|
427
|
+
file = fopen(filename, "r");
|
428
|
+
else
|
429
|
+
file = stdin;
|
430
|
+
|
431
|
+
if (file != NULL)
|
432
|
+
velvetLog("Reading raw file %s\n", filename);
|
433
|
+
else
|
434
|
+
exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
|
435
|
+
|
436
|
+
while(fgets(line, maxline, file)) {
|
437
|
+
if (strlen(line) >= maxline - 1) {
|
438
|
+
velvetLog("Raw sequence files cannot contain reads longer than %i bp\n", maxline - 1);
|
439
|
+
#ifdef DEBUG
|
440
|
+
abort();
|
441
|
+
#endif
|
442
|
+
exit(1);
|
443
|
+
}
|
444
|
+
|
445
|
+
writeSeqName("RAW", seqWriteInfo, cat, sequenceIndex);
|
446
|
+
writeSequence(line, seqWriteInfo);
|
447
|
+
counter++;
|
448
|
+
}
|
449
|
+
fclose(file);
|
450
|
+
cleanupFastX(seqWriteInfo, cat);
|
451
|
+
velvetLog("%li reads found.\n", (long) counter);
|
452
|
+
velvetLog("Done\n");
|
453
|
+
}
|
454
|
+
|
455
|
+
// Imports sequences from a zipped raw file
|
456
|
+
// Memory space allocated within this function.
|
457
|
+
static void readRawGZFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex)
|
458
|
+
{
|
459
|
+
gzFile file;
|
460
|
+
const int maxline = 5000;
|
461
|
+
char line[5000];
|
462
|
+
IDnum counter = 0;
|
463
|
+
|
464
|
+
initFastX(seqWriteInfo, cat);
|
465
|
+
if (strcmp(filename, "-"))
|
466
|
+
file = gzopen(filename, "rb");
|
467
|
+
else {
|
468
|
+
file = gzdopen(fileno(stdin), "rb");
|
469
|
+
SET_BINARY_MODE(stdin);
|
470
|
+
}
|
471
|
+
|
472
|
+
if (file != NULL)
|
473
|
+
velvetLog("Reading zipped raw sequence file %s\n", filename);
|
474
|
+
else
|
475
|
+
exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
|
476
|
+
|
477
|
+
while(gzgets(file, line, maxline)) {
|
478
|
+
if (strlen(line) >= maxline - 1) {
|
479
|
+
velvetLog("Raw sequence files cannot contain reads longer than %i bp\n", maxline - 1);
|
480
|
+
#ifdef DEBUG
|
481
|
+
abort();
|
482
|
+
#endif
|
483
|
+
exit(1);
|
484
|
+
}
|
485
|
+
|
486
|
+
writeSeqName("RAW", seqWriteInfo, cat, sequenceIndex);
|
487
|
+
writeSequence(line, seqWriteInfo);
|
488
|
+
counter++;
|
489
|
+
}
|
490
|
+
gzclose(file);
|
491
|
+
cleanupFastX(seqWriteInfo, cat);
|
492
|
+
velvetLog("%li reads found.\n", (long) counter);
|
493
|
+
velvetLog("Done\n");
|
494
|
+
}
|
495
|
+
|
496
|
+
static void fillReferenceCoordinateTable(char *filename, ReferenceCoordinateTable * refCoords, IDnum counter)
|
497
|
+
{
|
498
|
+
FILE *file;
|
499
|
+
const int maxline = 5000;
|
500
|
+
char line[5000];
|
501
|
+
char * name;
|
502
|
+
long long start, finish;
|
503
|
+
Coordinate i;
|
504
|
+
IDnum index = 0;
|
505
|
+
|
506
|
+
if (strcmp(filename, "-") == 0)
|
507
|
+
exitErrorf(EXIT_FAILURE, false, "Cannot read reference sequence from stdin");
|
508
|
+
else
|
509
|
+
file = fopen(filename, "r");
|
510
|
+
|
511
|
+
if (counter == 0)
|
512
|
+
return;
|
513
|
+
|
514
|
+
resizeReferenceCoordinateTable(refCoords,counter);
|
515
|
+
|
516
|
+
while (fgets(line, maxline, file) && index < counter) {
|
517
|
+
if (line[0] == '>') {
|
518
|
+
name = callocOrExit(strlen(line), char);
|
519
|
+
|
520
|
+
if (strchr(line, ':')) {
|
521
|
+
sscanf(strtok(line, ":-\r\n\t "), ">%s", name);
|
522
|
+
sscanf(strtok(NULL, ":-\r\n\t "), "%lli", &start);
|
523
|
+
sscanf(strtok(NULL, ":-\r\n\t "), "%lli", &finish);
|
524
|
+
if (start <= finish)
|
525
|
+
addReferenceCoordinate(refCoords, name, start, finish, true);
|
526
|
+
else
|
527
|
+
addReferenceCoordinate(refCoords, name, finish, start, false);
|
528
|
+
} else {
|
529
|
+
// Chomping EOL characters and comments
|
530
|
+
for (i=strlen(line) - 1; i >= 0; i--)
|
531
|
+
if (line[i] == '\n' || line[i] == '\r' || line[i] == ' ' || line[i] == '\t')
|
532
|
+
line[i] = '\0';
|
533
|
+
|
534
|
+
strcpy(name, line + 1);
|
535
|
+
addReferenceCoordinate(refCoords, name, 1, -1, true);
|
536
|
+
}
|
537
|
+
|
538
|
+
index++;
|
539
|
+
}
|
540
|
+
}
|
541
|
+
|
542
|
+
sortReferenceCoordinateTable(refCoords);
|
543
|
+
}
|
544
|
+
|
545
|
+
#define FASTQ 1
|
546
|
+
#define FASTA 2
|
547
|
+
#define FASTA_GZ 5
|
548
|
+
#define FASTQ_GZ 6
|
549
|
+
#define SAM 8
|
550
|
+
#define BAM 9
|
551
|
+
#define RAW 10
|
552
|
+
#define RAW_GZ 11
|
553
|
+
#define AUTO 12
|
554
|
+
|
555
|
+
static gzFile openFastXFile(int fileType, char*filename)
|
556
|
+
{
|
557
|
+
gzFile file;
|
558
|
+
char c;
|
559
|
+
|
560
|
+
// Choose file or stdin
|
561
|
+
if (strcmp(filename, "-")==0) {
|
562
|
+
file = gzdopen(fileno(stdin), "rb");
|
563
|
+
SET_BINARY_MODE(stdin);
|
564
|
+
} else {
|
565
|
+
file = gzopen(filename, "rb");
|
566
|
+
}
|
567
|
+
|
568
|
+
// Verify filetype
|
569
|
+
c = gzgetc(file);
|
570
|
+
switch (fileType) {
|
571
|
+
case FASTA:
|
572
|
+
case FASTA_GZ:
|
573
|
+
if (c != EOF && c!='>')
|
574
|
+
exitErrorf(EXIT_FAILURE, false, "%s does not seem to be in FastA format", filename);
|
575
|
+
break;
|
576
|
+
case FASTQ:
|
577
|
+
case FASTQ_GZ:
|
578
|
+
if (c != EOF && c!='@')
|
579
|
+
exitErrorf(EXIT_FAILURE, false, "%s does not seem to be in FastQ format", filename);
|
580
|
+
break;
|
581
|
+
}
|
582
|
+
gzungetc(c, file);
|
583
|
+
|
584
|
+
|
585
|
+
if (file != NULL) {
|
586
|
+
char *type;
|
587
|
+
switch (fileType) {
|
588
|
+
case FASTA:
|
589
|
+
case FASTA_GZ: type = "FastA"; break;
|
590
|
+
case FASTQ:
|
591
|
+
case FASTQ_GZ: type = "FastQ"; break;
|
592
|
+
default: type = ""; break;
|
593
|
+
}
|
594
|
+
velvetLog("Reading %s file %s;\n", type, filename);
|
595
|
+
} else
|
596
|
+
exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
|
597
|
+
|
598
|
+
return file;
|
599
|
+
}
|
600
|
+
|
601
|
+
typedef struct {
|
602
|
+
gzFile gzFile;
|
603
|
+
AutoFile *autoFile;
|
604
|
+
} FileGZOrAuto;
|
605
|
+
|
606
|
+
size_t fileGZOrAuto_read(FileGZOrAuto kseq_file, void *ptr, size_t size)
|
607
|
+
{
|
608
|
+
if (kseq_file.gzFile)
|
609
|
+
return gzread(kseq_file.gzFile, ptr, size);
|
610
|
+
else
|
611
|
+
return fread(ptr, 1, size, kseq_file.autoFile->file);
|
612
|
+
}
|
613
|
+
|
614
|
+
void fileGZOrAuto_close(FileGZOrAuto kseq_file)
|
615
|
+
{
|
616
|
+
if (kseq_file.gzFile)
|
617
|
+
gzclose(kseq_file.gzFile);
|
618
|
+
else
|
619
|
+
closeFileAuto(kseq_file.autoFile);
|
620
|
+
}
|
621
|
+
|
622
|
+
char const* charToType(char c)
|
623
|
+
{
|
624
|
+
switch(c) {
|
625
|
+
case '>': return "FastA";
|
626
|
+
case '@': return "FastQ";
|
627
|
+
default: return "Unknown";
|
628
|
+
}
|
629
|
+
}
|
630
|
+
|
631
|
+
// Define mode to use kseq in
|
632
|
+
KSEQ_INIT(FileGZOrAuto, fileGZOrAuto_read)
|
633
|
+
|
634
|
+
// Read in FastA or FastQ files in compressed or gz format
|
635
|
+
static void readFastXFile(int fileType, SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum * sequenceIndex, ReferenceCoordinateTable * refCoords)
|
636
|
+
{
|
637
|
+
kseq_t *seq;
|
638
|
+
FileGZOrAuto file;
|
639
|
+
IDnum counter = 0;
|
640
|
+
|
641
|
+
file.gzFile = file.autoFile = NULL;
|
642
|
+
if (fileType == AUTO) {
|
643
|
+
file.autoFile = openFileAuto(filename);
|
644
|
+
if (!file.autoFile)
|
645
|
+
exitErrorf(EXIT_FAILURE, false, "Unable to open file '%s' in auto mode", filename);
|
646
|
+
velvetLog("Reading file '%s' using '%s' as %s\n", filename, file.autoFile->decompressor, charToType(file.autoFile->first_char));
|
647
|
+
} else
|
648
|
+
file.gzFile = openFastXFile(fileType, filename);
|
649
|
+
|
650
|
+
initFastX(seqWriteInfo, cat);
|
651
|
+
// Read a sequence at a time
|
652
|
+
seq = kseq_init(file);
|
653
|
+
while (kseq_read(seq) >= 0) {
|
654
|
+
counter++;
|
655
|
+
writeSeqName(seq->name.s, seqWriteInfo, cat, sequenceIndex);
|
656
|
+
writeSequence(seq->seq.s, seqWriteInfo);
|
657
|
+
}
|
658
|
+
|
659
|
+
kseq_destroy(seq);
|
660
|
+
fileGZOrAuto_close(file);
|
661
|
+
|
662
|
+
if (cat == REFERENCE) {
|
663
|
+
fillReferenceCoordinateTable(filename, refCoords, counter);
|
664
|
+
}
|
665
|
+
cleanupFastX(seqWriteInfo, cat);
|
666
|
+
|
667
|
+
velvetLog("%li sequences found\n", (long) counter);
|
668
|
+
velvetLog("Done\n");
|
669
|
+
}
|
670
|
+
|
671
|
+
static void readFastXPair(int fileType, SequencesWriter *seqWriteInfo, char *filename1, char *filename2, Category cat, IDnum * sequenceIndex)
|
672
|
+
{
|
673
|
+
kseq_t *seq1, *seq2;
|
674
|
+
FileGZOrAuto file1, file2;
|
675
|
+
IDnum counter = 0;
|
676
|
+
|
677
|
+
if (cat==REFERENCE)
|
678
|
+
exitErrorf(EXIT_FAILURE, false, "Cannot read reference sequence in 'separate' read mode");
|
679
|
+
|
680
|
+
file1.gzFile = file1.autoFile = NULL;
|
681
|
+
file2.gzFile = file2.autoFile = NULL;
|
682
|
+
if (fileType == AUTO) {
|
683
|
+
file1.autoFile = openFileAuto(filename1);
|
684
|
+
if (!file1.autoFile)
|
685
|
+
exitErrorf(EXIT_FAILURE, false, "Unable to open file '%s' in auto mode", filename1);
|
686
|
+
velvetLog("Reading file '%s' using '%s' as %s\n", filename1, file1.autoFile->decompressor, charToType(file1.autoFile->first_char));
|
687
|
+
file2.autoFile = openFileAuto(filename2);
|
688
|
+
if (!file2.autoFile)
|
689
|
+
exitErrorf(EXIT_FAILURE, false, "Unable to open file '%s' in auto mode", filename2);
|
690
|
+
velvetLog("Reading file '%s' using '%s' as %s\n", filename2, file2.autoFile->decompressor, charToType(file2.autoFile->first_char));
|
691
|
+
} else {
|
692
|
+
file1.gzFile = openFastXFile(fileType, filename1);
|
693
|
+
file2.gzFile = openFastXFile(fileType, filename2);
|
694
|
+
}
|
695
|
+
initFastX(seqWriteInfo, cat);
|
696
|
+
|
697
|
+
// Read a sequence at a time
|
698
|
+
seq1 = kseq_init(file1);
|
699
|
+
seq2 = kseq_init(file2);
|
700
|
+
while (kseq_read(seq1) >= 0) {
|
701
|
+
counter++;
|
702
|
+
writeSeqName(seq1->name.s, seqWriteInfo, cat, sequenceIndex);
|
703
|
+
writeSequence(seq1->seq.s, seqWriteInfo);
|
704
|
+
|
705
|
+
if (kseq_read(seq2) < 0)
|
706
|
+
exitErrorf(EXIT_FAILURE, false, "Right sequence file '%s' has too few sequences", filename2);
|
707
|
+
|
708
|
+
counter++;
|
709
|
+
writeSeqName(seq2->name.s, seqWriteInfo, cat, sequenceIndex);
|
710
|
+
writeSequence(seq2->seq.s, seqWriteInfo);
|
711
|
+
}
|
712
|
+
if (kseq_read(seq2) >= 0)
|
713
|
+
exitErrorf(EXIT_FAILURE, false, "Right sequence file '%s' has too many sequences", filename2);
|
714
|
+
|
715
|
+
kseq_destroy(seq1);
|
716
|
+
kseq_destroy(seq2);
|
717
|
+
|
718
|
+
fileGZOrAuto_close(file1);
|
719
|
+
fileGZOrAuto_close(file2);
|
720
|
+
|
721
|
+
cleanupFastX(seqWriteInfo, cat);
|
722
|
+
|
723
|
+
velvetLog("%li sequences found in total in the paired sequence files\n", (long) counter);
|
724
|
+
velvetLog("Done\n");
|
725
|
+
}
|
726
|
+
|
727
|
+
static void addMapping(boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) {
|
728
|
+
if (isCreateBinary()) {
|
729
|
+
seqWriteInfo->m_bIsRef = true;
|
730
|
+
RefInfoList *refElem = callocOrExit(1, RefInfoList);
|
731
|
+
if (refCoord->positive_strand) {
|
732
|
+
refElem->m_elem.m_referenceID = (long) orientation * refCoord->referenceID;
|
733
|
+
refElem->m_elem.m_pos = (long long) (pos - refCoord->start);
|
734
|
+
} else {
|
735
|
+
refElem->m_elem.m_referenceID = (long) -orientation * refCoord->referenceID;
|
736
|
+
refElem->m_elem.m_pos = (long long) (refCoord->finish - pos - strlen(seq));
|
737
|
+
}
|
738
|
+
refElem->next = NULL;
|
739
|
+
if (seqWriteInfo->m_refInfoHead == NULL) {
|
740
|
+
seqWriteInfo->m_refInfoHead = refElem;
|
741
|
+
} else {
|
742
|
+
(*refTail)->next = refElem;
|
743
|
+
}
|
744
|
+
*refTail = refElem;
|
745
|
+
seqWriteInfo->m_refCnt++;
|
746
|
+
} else {
|
747
|
+
if (refCoord->positive_strand) {
|
748
|
+
snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) orientation * refCoord->referenceID, (long long) (pos - refCoord->start));
|
749
|
+
} else
|
750
|
+
snprintf(buffer, *buffer_size, "%sM\t%li\t%lli\n", buffer, (long) - orientation * refCoord->referenceID, (long long) (refCoord->finish - pos - strlen(seq)));
|
751
|
+
|
752
|
+
if (*buffer_size - strlen(buffer) < 100) {
|
753
|
+
*buffer_size += 1000;
|
754
|
+
buffer = reallocOrExit(buffer, *buffer_size, char);
|
755
|
+
}
|
756
|
+
}
|
757
|
+
|
758
|
+
// Increment counter
|
759
|
+
refCoord->counter++;
|
760
|
+
}
|
761
|
+
|
762
|
+
static void writeMappedSequence(IDnum * sequenceIndex, Category cat, Category prev_cat, char * previous_seq, char * previous_qname, char * previous_qname_pairing, char * buffer, SequencesWriter * seqWriteInfo) {
|
763
|
+
char print_qname[5000];
|
764
|
+
if (isCreateBinary()) {
|
765
|
+
if (prev_cat != cat) {
|
766
|
+
inputCnySeqFileStart(cat, seqWriteInfo);
|
767
|
+
prev_cat = cat;
|
768
|
+
}
|
769
|
+
cnySeqInsertStart(seqWriteInfo);
|
770
|
+
cnySeqInsertNucleotideString(previous_seq, seqWriteInfo);
|
771
|
+
sprintf(print_qname, ">%s%s", previous_qname, previous_qname_pairing);
|
772
|
+
cnySeqInsertSequenceName(print_qname, (long) ((*sequenceIndex)++), seqWriteInfo, cat);
|
773
|
+
cnySeqInsertEnd(seqWriteInfo);
|
774
|
+
} else {
|
775
|
+
velvetFprintf(seqWriteInfo->m_pFile, ">%s%s\t%ld\t%d\n", previous_qname, previous_qname_pairing,
|
776
|
+
(long) ((*sequenceIndex)++), (int) cat);
|
777
|
+
writeFastaSequence(seqWriteInfo->m_pFile, previous_seq);
|
778
|
+
velvetFprintf(seqWriteInfo->m_pFile, "%s", buffer);
|
779
|
+
strcpy(buffer, "");
|
780
|
+
}
|
781
|
+
}
|
782
|
+
|
783
|
+
static void readCigar(char * cigar, boolean orientation, Coordinate pos, char * seq, ReferenceCoordinate * refCoord, char * buffer, SequencesWriter * seqWriteInfo, RefInfoList ** refTail, size_t * buffer_size) {
|
784
|
+
long long cigar_num;
|
785
|
+
int cigar_index;
|
786
|
+
char c;
|
787
|
+
|
788
|
+
if (strlen(cigar) == 1 && cigar[0] == '*')
|
789
|
+
;
|
790
|
+
else {
|
791
|
+
cigar_num = 0;
|
792
|
+
for (cigar_index = 0; cigar_index < strlen(cigar); cigar_index++) {
|
793
|
+
c = cigar[cigar_index];
|
794
|
+
if (c == 'M' || c == '=' || c == 'X') {
|
795
|
+
if (refCoord->finish < 0 || pos < refCoord->finish)
|
796
|
+
addMapping(orientation, pos, seq, refCoord, buffer, seqWriteInfo, refTail, buffer_size);
|
797
|
+
cigar_num = 0;
|
798
|
+
} else if (c == 'S' || c == 'I') {
|
799
|
+
pos -= cigar_num;
|
800
|
+
cigar_num = 0;
|
801
|
+
} else if (c == 'D' || c == 'N') {
|
802
|
+
pos += cigar_num;
|
803
|
+
cigar_num = 0;
|
804
|
+
} else if (c == 'H' || c == 'P') {
|
805
|
+
cigar_num = 0;
|
806
|
+
} else if (isdigit(c)) {
|
807
|
+
cigar_num = 10 * cigar_num + (c - 48);
|
808
|
+
} else {
|
809
|
+
abort();
|
810
|
+
}
|
811
|
+
}
|
812
|
+
}
|
813
|
+
}
|
814
|
+
|
815
|
+
static void readSAMFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)
|
816
|
+
{
|
817
|
+
char line[5000];
|
818
|
+
unsigned long lineno;
|
819
|
+
IDnum readCount = 0;
|
820
|
+
char previous_qname_pairing[10];
|
821
|
+
char previous_qname[5000];
|
822
|
+
char previous_seq[5000];
|
823
|
+
boolean previous_paired = false;
|
824
|
+
Category prev_cat = cat;
|
825
|
+
Category apparentCat;
|
826
|
+
ReferenceCoordinate * refCoord;
|
827
|
+
RefInfoList *refTail = NULL;
|
828
|
+
seqWriteInfo->m_referenceMask = NULL; // no ref masks for SAM/BAM
|
829
|
+
seqWriteInfo->m_position = 0;
|
830
|
+
seqWriteInfo->m_openMask = false;
|
831
|
+
|
832
|
+
size_t buffer_size = 5000;
|
833
|
+
char * buffer = callocOrExit(buffer_size, char);
|
834
|
+
|
835
|
+
if (cat == REFERENCE) {
|
836
|
+
velvetLog("SAM file %s cannot contain reference sequences.\n", filename);
|
837
|
+
velvetLog("Please check the command line.\n");
|
838
|
+
#ifdef DEBUG
|
839
|
+
abort();
|
840
|
+
#endif
|
841
|
+
exit(1);
|
842
|
+
}
|
843
|
+
|
844
|
+
FILE *file = (strcmp(filename, "-") != 0)? fopen(filename, "r") : stdin;
|
845
|
+
if (file)
|
846
|
+
velvetLog("Reading SAM file %s\n", filename);
|
847
|
+
else
|
848
|
+
exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
|
849
|
+
if (isCreateBinary()) {
|
850
|
+
inputCnySeqFileStart(cat, seqWriteInfo);
|
851
|
+
}
|
852
|
+
strcpy(previous_qname, "");
|
853
|
+
for (lineno = 1; fgets(line, sizeof(line), file); lineno++) {
|
854
|
+
if (line[0] != '@') {
|
855
|
+
char *qname, *flag, *seq, *rname, *cigar;
|
856
|
+
long long pos;
|
857
|
+
int orientation;
|
858
|
+
int i;
|
859
|
+
|
860
|
+
qname = strtok(line, "\t");
|
861
|
+
flag = strtok(NULL, "\t");
|
862
|
+
rname = strtok(NULL, "\t");
|
863
|
+
sscanf(strtok(NULL, "\t"), "%lli", &pos);
|
864
|
+
orientation = 1;
|
865
|
+
|
866
|
+
// Mapping scor
|
867
|
+
(void) strtok(NULL, "\t");
|
868
|
+
cigar = strtok(NULL, "\t");
|
869
|
+
|
870
|
+
// Columns 7,8,9 are paired name, position and score
|
871
|
+
for (i = 7; i < 10; i++)
|
872
|
+
(void) strtok(NULL, "\t");
|
873
|
+
seq = strtok(NULL, "\t");
|
874
|
+
|
875
|
+
if (seq == NULL) {
|
876
|
+
velvetFprintf(stderr,
|
877
|
+
"Line #%lu: ignoring SAM record with too few fields\n",
|
878
|
+
lineno);
|
879
|
+
}
|
880
|
+
else if (strcmp(seq, "*") == 0) {
|
881
|
+
velvetFprintf(stderr,
|
882
|
+
"Line #%lu: ignoring SAM record with omitted SEQ field\n",
|
883
|
+
lineno);
|
884
|
+
}
|
885
|
+
else {
|
886
|
+
// Accept flags represented in either decimal or hex:
|
887
|
+
int flagbits = strtol(flag, NULL, 0);
|
888
|
+
|
889
|
+
if (flagbits & 0x4)
|
890
|
+
strcpy(rname, "");
|
891
|
+
|
892
|
+
const char *qname_pairing = "";
|
893
|
+
if (flagbits & 0x40)
|
894
|
+
qname_pairing = "/1";
|
895
|
+
else if (flagbits & 0x80)
|
896
|
+
qname_pairing = "/2";
|
897
|
+
|
898
|
+
if (flagbits & 0x10) {
|
899
|
+
orientation = -1;
|
900
|
+
reverseComplementSequence(seq);
|
901
|
+
}
|
902
|
+
|
903
|
+
// Determine if paired to previous read
|
904
|
+
boolean same_name = (strcmp(qname, previous_qname) == 0);
|
905
|
+
if (readCount && (!same_name || strcmp(qname_pairing, previous_qname_pairing) != 0)) {
|
906
|
+
if (cat % 2 && !same_name && !previous_paired)
|
907
|
+
apparentCat = cat - 1;
|
908
|
+
else
|
909
|
+
apparentCat = cat;
|
910
|
+
|
911
|
+
previous_paired = (cat % 2 && same_name);
|
912
|
+
|
913
|
+
writeMappedSequence(sequenceIndex, apparentCat, prev_cat, previous_seq, previous_qname, previous_qname_pairing, buffer, seqWriteInfo);
|
914
|
+
prev_cat = apparentCat;
|
915
|
+
}
|
916
|
+
|
917
|
+
if (!(flagbits & 0x4) && (refCoord = findReferenceCoordinate(refCoords, rname, (Coordinate) pos, (Coordinate) pos + strlen(seq) - 1, orientation))) {
|
918
|
+
readCigar(cigar, orientation, pos, seq, refCoord, buffer, seqWriteInfo, &refTail, &buffer_size);
|
919
|
+
}
|
920
|
+
|
921
|
+
strcpy(previous_qname, qname);
|
922
|
+
strcpy(previous_qname_pairing, qname_pairing);
|
923
|
+
strcpy(previous_seq, seq);
|
924
|
+
velvetifySequence(previous_seq, seqWriteInfo);
|
925
|
+
|
926
|
+
readCount++;
|
927
|
+
}
|
928
|
+
}
|
929
|
+
}
|
930
|
+
|
931
|
+
if (readCount) {
|
932
|
+
if (cat % 2 && !previous_paired)
|
933
|
+
apparentCat = cat - 1;
|
934
|
+
else
|
935
|
+
apparentCat = cat;
|
936
|
+
writeMappedSequence(sequenceIndex, apparentCat, prev_cat, previous_seq, previous_qname, previous_qname_pairing, buffer, seqWriteInfo);
|
937
|
+
}
|
938
|
+
|
939
|
+
free(buffer);
|
940
|
+
fclose(file);
|
941
|
+
velvetLog("%lu reads found.\n", (long) readCount);
|
942
|
+
velvetLog("Done\n");
|
943
|
+
}
|
944
|
+
|
945
|
+
static int readBAMint32(gzFile file)
|
946
|
+
{
|
947
|
+
unsigned char buffer[4];
|
948
|
+
if (gzread(file, buffer, 4) != 4)
|
949
|
+
exitErrorf(EXIT_FAILURE, false, "BAM file header truncated");
|
950
|
+
|
951
|
+
return int32(buffer);
|
952
|
+
}
|
953
|
+
|
954
|
+
static void readBAMFile(SequencesWriter *seqWriteInfo, char *filename, Category cat, IDnum *sequenceIndex, ReferenceCoordinateTable * refCoords)
|
955
|
+
{
|
956
|
+
size_t seqCapacity = 0;
|
957
|
+
char *seq = NULL;
|
958
|
+
char cigar[5000];
|
959
|
+
char cigar_buffer[5000];
|
960
|
+
size_t bufferCapacity = 4;
|
961
|
+
unsigned char *buffer = mallocOrExit(bufferCapacity, unsigned char);
|
962
|
+
unsigned long recno, readCount;
|
963
|
+
int i, refCount;
|
964
|
+
gzFile file;
|
965
|
+
char previous_qname_pairing[10];
|
966
|
+
char previous_qname[5000];
|
967
|
+
char previous_seq[5000];
|
968
|
+
boolean previous_paired = false;
|
969
|
+
Category prev_cat = cat;
|
970
|
+
Category apparentCat;
|
971
|
+
char ** refNames;
|
972
|
+
ReferenceCoordinate * refCoord;
|
973
|
+
seqWriteInfo->m_referenceMask = NULL; // no ref masks for SAM/BAM
|
974
|
+
seqWriteInfo->m_position = 0;
|
975
|
+
seqWriteInfo->m_openMask = false;
|
976
|
+
|
977
|
+
RefInfoList *refTail = NULL;
|
978
|
+
size_t mapBuffer_size = 1000;
|
979
|
+
char * mapBuffer = callocOrExit(mapBuffer_size, char);
|
980
|
+
|
981
|
+
if (cat == REFERENCE) {
|
982
|
+
velvetLog("BAM file %s cannot contain reference sequences.\n", filename);
|
983
|
+
velvetLog("Please check the command line.\n");
|
984
|
+
#ifdef DEBUG
|
985
|
+
abort();
|
986
|
+
#endif
|
987
|
+
exit(1);
|
988
|
+
}
|
989
|
+
|
990
|
+
if (strcmp(filename, "-") != 0)
|
991
|
+
file = gzopen(filename, "rb");
|
992
|
+
else {
|
993
|
+
file = gzdopen(fileno(stdin), "rb");
|
994
|
+
SET_BINARY_MODE(stdin);
|
995
|
+
}
|
996
|
+
|
997
|
+
if (file != NULL)
|
998
|
+
velvetLog("Reading BAM file %s\n", filename);
|
999
|
+
else
|
1000
|
+
exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
|
1001
|
+
|
1002
|
+
if (! (gzread(file, buffer, 4) == 4 && memcmp(buffer, "BAM\1", 4) == 0))
|
1003
|
+
exitErrorf(EXIT_FAILURE, false, "%s is not in BAM format", filename);
|
1004
|
+
|
1005
|
+
// Skip header text
|
1006
|
+
if (gzseek(file, readBAMint32(file), SEEK_CUR) == -1)
|
1007
|
+
exitErrorf(EXIT_FAILURE, false, "gzseek failed");
|
1008
|
+
|
1009
|
+
// Skip header reference list
|
1010
|
+
refCount = readBAMint32(file);
|
1011
|
+
refNames = callocOrExit(refCount, char *);
|
1012
|
+
for (i = 0; i < refCount; i++) {
|
1013
|
+
int strLength;
|
1014
|
+
|
1015
|
+
if (gzread(file, buffer, 4) != 4)
|
1016
|
+
exitErrorf(EXIT_FAILURE, false, "BAM alignment record truncated");
|
1017
|
+
|
1018
|
+
strLength = int32(buffer);
|
1019
|
+
refNames[i] = callocOrExit(strLength, char);
|
1020
|
+
|
1021
|
+
if (bufferCapacity < 4 + strLength) {
|
1022
|
+
bufferCapacity = 4 + strLength + 4096;
|
1023
|
+
buffer = reallocOrExit(buffer, bufferCapacity, unsigned char);
|
1024
|
+
}
|
1025
|
+
|
1026
|
+
if (gzread(file, buffer, 4 + strLength) != 4 + strLength)
|
1027
|
+
exitErrorf(EXIT_FAILURE, false, "BAM alignment record truncated");
|
1028
|
+
|
1029
|
+
strcpy(refNames[i], (char *) buffer);
|
1030
|
+
}
|
1031
|
+
if (isCreateBinary()) {
|
1032
|
+
inputCnySeqFileStart(cat, seqWriteInfo);
|
1033
|
+
}
|
1034
|
+
strcpy(previous_qname, "");
|
1035
|
+
readCount = 0;
|
1036
|
+
for (recno = 1; gzread(file, buffer, 4) == 4; recno++) {
|
1037
|
+
int blockSize = int32(buffer);
|
1038
|
+
int readLength;
|
1039
|
+
|
1040
|
+
if (bufferCapacity < 4 + blockSize) {
|
1041
|
+
bufferCapacity = 4 + blockSize + 4096;
|
1042
|
+
buffer = reallocOrExit(buffer, bufferCapacity, unsigned char);
|
1043
|
+
}
|
1044
|
+
|
1045
|
+
if (gzread(file, &buffer[4], blockSize) != blockSize)
|
1046
|
+
exitErrorf(EXIT_FAILURE, false, "BAM alignment record truncated");
|
1047
|
+
|
1048
|
+
readLength = int32(&buffer[20]);
|
1049
|
+
if (readLength == 0) {
|
1050
|
+
velvetFprintf(stderr,
|
1051
|
+
"Record #%lu: ignoring BAM record with omitted SEQ field\n",
|
1052
|
+
recno);
|
1053
|
+
}
|
1054
|
+
else {
|
1055
|
+
int readNameLength = buffer[12];
|
1056
|
+
int flag_nc = int32(&buffer[16]);
|
1057
|
+
int flagbits = flag_nc >> 16;
|
1058
|
+
int cigarLength = flag_nc & 0xffff;
|
1059
|
+
char *qname = (char *)&buffer[36];
|
1060
|
+
uint32_t *rawcigar = (uint32_t *) &buffer[36 + readNameLength];
|
1061
|
+
unsigned char *rawseq =
|
1062
|
+
&buffer[36 + readNameLength + 4 * cigarLength];
|
1063
|
+
int rID = int32(&buffer[4]);
|
1064
|
+
// NOTE: BAM file coords are 0-based, not 1-based like SAM files
|
1065
|
+
// No comment
|
1066
|
+
long long pos = int32(&buffer[8]) + 1;
|
1067
|
+
int orientation = 1;
|
1068
|
+
|
1069
|
+
const char *qname_pairing = "";
|
1070
|
+
if (flagbits & 0x40)
|
1071
|
+
qname_pairing = "/1";
|
1072
|
+
else if (flagbits & 0x80)
|
1073
|
+
qname_pairing = "/2";
|
1074
|
+
|
1075
|
+
strcpy(cigar, "");
|
1076
|
+
for (i = 0; i < cigarLength; i++) {
|
1077
|
+
static const char decode_ops[] = "MIDNSHP=X";
|
1078
|
+
uint32_t packed = *(rawcigar++);
|
1079
|
+
sprintf(cigar_buffer, "%i%c", packed >> 4, decode_ops[packed & 0xf]);
|
1080
|
+
strcat(cigar, cigar_buffer);
|
1081
|
+
}
|
1082
|
+
|
1083
|
+
if (seqCapacity < readLength + 1) {
|
1084
|
+
seqCapacity = readLength * 2 + 1;
|
1085
|
+
seq = reallocOrExit(seq, seqCapacity, char);
|
1086
|
+
}
|
1087
|
+
|
1088
|
+
for (i = 0; i < readLength; i += 2) {
|
1089
|
+
static const char decode_bases[] = "=ACMGRSVTWYHKDBN";
|
1090
|
+
unsigned int packed = *(rawseq++);
|
1091
|
+
seq[i] = decode_bases[packed >> 4];
|
1092
|
+
seq[i+1] = decode_bases[packed & 0xf];
|
1093
|
+
}
|
1094
|
+
seq[readLength] = '\0';
|
1095
|
+
|
1096
|
+
if (flagbits & 0x10) {
|
1097
|
+
orientation = -1;
|
1098
|
+
reverseComplementSequence(seq);
|
1099
|
+
}
|
1100
|
+
|
1101
|
+
// Determine if paired to previous read
|
1102
|
+
boolean same_name = (strcmp(qname, previous_qname) == 0);
|
1103
|
+
if (readCount > 0 && (!same_name || strcmp(qname_pairing, previous_qname_pairing) != 0)) {
|
1104
|
+
if (cat % 2 && !same_name && !previous_paired)
|
1105
|
+
apparentCat = cat - 1;
|
1106
|
+
else
|
1107
|
+
apparentCat = cat;
|
1108
|
+
|
1109
|
+
previous_paired = (cat % 2 && same_name);
|
1110
|
+
|
1111
|
+
writeMappedSequence(sequenceIndex, apparentCat, prev_cat, previous_seq, previous_qname, previous_qname_pairing, mapBuffer, seqWriteInfo);
|
1112
|
+
prev_cat = apparentCat;
|
1113
|
+
}
|
1114
|
+
|
1115
|
+
if (!(flagbits & 0x4) && (refCoord = findReferenceCoordinate(refCoords, refNames[rID], (Coordinate) pos, (Coordinate) pos + strlen(seq) - 1, orientation)))
|
1116
|
+
readCigar(cigar, orientation, pos, seq, refCoord, mapBuffer, seqWriteInfo, &refTail, &mapBuffer_size);
|
1117
|
+
|
1118
|
+
strcpy(previous_qname, qname);
|
1119
|
+
strcpy(previous_qname_pairing, qname_pairing);
|
1120
|
+
strcpy(previous_seq, seq);
|
1121
|
+
velvetifySequence(previous_seq, seqWriteInfo);
|
1122
|
+
|
1123
|
+
readCount++;
|
1124
|
+
}
|
1125
|
+
}
|
1126
|
+
|
1127
|
+
if (readCount) {
|
1128
|
+
if (cat % 2 && !previous_paired)
|
1129
|
+
apparentCat = cat - 1;
|
1130
|
+
else
|
1131
|
+
apparentCat = cat;
|
1132
|
+
writeMappedSequence(sequenceIndex, apparentCat, prev_cat, previous_seq, previous_qname, previous_qname_pairing, mapBuffer, seqWriteInfo);
|
1133
|
+
}
|
1134
|
+
|
1135
|
+
free(seq);
|
1136
|
+
free(buffer);
|
1137
|
+
free(mapBuffer);
|
1138
|
+
|
1139
|
+
gzclose(file);
|
1140
|
+
velvetLog("%lu reads found.\n", readCount);
|
1141
|
+
velvetLog("Done\n");
|
1142
|
+
}
|
1143
|
+
|
1144
|
+
|
1145
|
+
static void printUsage()
|
1146
|
+
{
|
1147
|
+
puts("Usage:");
|
1148
|
+
puts("./velveth directory hash_length {[-file_format][-read_type][-separate|-interleaved] filename} [options]");
|
1149
|
+
puts("");
|
1150
|
+
puts("\tdirectory\t\t: directory name for output files");
|
1151
|
+
printf("\thash_length\t\t: odd integer (if even, it will be decremented) <= %i (if above, will be reduced)\n", MAXKMERLENGTH);
|
1152
|
+
puts("\tfilename\t\t: path to sequence file or - for standard input");
|
1153
|
+
puts("");
|
1154
|
+
puts("File format options:");
|
1155
|
+
puts("\t-fasta");
|
1156
|
+
puts("\t-fastq");
|
1157
|
+
puts("\t-raw");
|
1158
|
+
puts("\t-fasta.gz");
|
1159
|
+
puts("\t-fastq.gz");
|
1160
|
+
puts("\t-raw.gz");
|
1161
|
+
puts("\t-sam");
|
1162
|
+
puts("\t-bam");
|
1163
|
+
puts("\t-fmtAuto");
|
1164
|
+
puts("");
|
1165
|
+
puts("Read type options:");
|
1166
|
+
puts("\t-short");
|
1167
|
+
puts("\t-shortPaired");
|
1168
|
+
puts("\t-short2");
|
1169
|
+
puts("\t-shortPaired2");
|
1170
|
+
puts("\t-long");
|
1171
|
+
puts("\t-longPaired");
|
1172
|
+
puts("\t-reference");
|
1173
|
+
puts("");
|
1174
|
+
puts("Options:");
|
1175
|
+
puts("\t-strand_specific\t: for strand specific transcriptome sequencing data (default: off)");
|
1176
|
+
puts("");
|
1177
|
+
puts("Output:");
|
1178
|
+
puts("\tdirectory/Roadmaps");
|
1179
|
+
puts("\tdirectory/Sequences");
|
1180
|
+
puts("\t\t[Both files are picked up by graph, so please leave them there]");
|
1181
|
+
}
|
1182
|
+
|
1183
|
+
// General argument parser for most functions
|
1184
|
+
// Basically a reused portion of toplevel code dumped into here
|
1185
|
+
void parseDataAndReadFiles(char * filename, int argc, char **argv, boolean * double_strand, boolean * noHash)
|
1186
|
+
{
|
1187
|
+
int argIndex = 1;
|
1188
|
+
int filetype = FASTA;
|
1189
|
+
Category cat = 0;
|
1190
|
+
IDnum sequenceIndex = 1;
|
1191
|
+
short short_var;
|
1192
|
+
ReferenceCoordinateTable * refCoords = newReferenceCoordinateTable();
|
1193
|
+
boolean reuseSequences = false;
|
1194
|
+
boolean separate_pair_files = false;
|
1195
|
+
|
1196
|
+
if (argc < 2) {
|
1197
|
+
printUsage();
|
1198
|
+
#ifdef DEBUG
|
1199
|
+
abort();
|
1200
|
+
#endif
|
1201
|
+
exit(1);
|
1202
|
+
}
|
1203
|
+
|
1204
|
+
for (argIndex = 1; argIndex < argc; argIndex++) {
|
1205
|
+
if (strcmp(argv[argIndex], "-strand_specific") == 0) {
|
1206
|
+
*double_strand = false;
|
1207
|
+
reference_coordinate_double_strand = false;
|
1208
|
+
} else if (strcmp(argv[argIndex], "-reuse_Sequences") == 0) {
|
1209
|
+
reuseSequences = true;
|
1210
|
+
} else if (strcmp(argv[argIndex], "-reuse_binary") == 0) {
|
1211
|
+
reuseSequences = true;
|
1212
|
+
} else if (strcmp(argv[argIndex], "-noHash") == 0) {
|
1213
|
+
*noHash = true;
|
1214
|
+
}
|
1215
|
+
}
|
1216
|
+
|
1217
|
+
if (reuseSequences)
|
1218
|
+
return;
|
1219
|
+
|
1220
|
+
SequencesWriter * seqWriteInfo = NULL;
|
1221
|
+
if (isCreateBinary()) {
|
1222
|
+
seqWriteInfo = openCnySeqForWrite(filename);
|
1223
|
+
seqWriteInfo->m_unifiedSeqFileHeader.m_bDoubleStrand = *double_strand;
|
1224
|
+
// file is already open
|
1225
|
+
} else {
|
1226
|
+
seqWriteInfo = callocOrExit(1, SequencesWriter);
|
1227
|
+
seqWriteInfo->m_pFile = fopen(filename, "w");
|
1228
|
+
}
|
1229
|
+
|
1230
|
+
for (argIndex = 1; argIndex < argc; argIndex++) {
|
1231
|
+
if (argv[argIndex][0] == '-' && strlen(argv[argIndex]) > 1) {
|
1232
|
+
|
1233
|
+
if (strcmp(argv[argIndex], "-fastq") == 0)
|
1234
|
+
filetype = FASTQ;
|
1235
|
+
else if (strcmp(argv[argIndex], "-fasta") == 0)
|
1236
|
+
filetype = FASTA;
|
1237
|
+
else if (strcmp(argv[argIndex], "-fastq.gz") == 0)
|
1238
|
+
filetype = FASTQ_GZ;
|
1239
|
+
else if (strcmp(argv[argIndex], "-fasta.gz") == 0)
|
1240
|
+
filetype = FASTA_GZ;
|
1241
|
+
else if (strcmp(argv[argIndex], "-sam") == 0)
|
1242
|
+
filetype = SAM;
|
1243
|
+
else if (strcmp(argv[argIndex], "-bam") == 0)
|
1244
|
+
filetype = BAM;
|
1245
|
+
else if (strcmp(argv[argIndex], "-raw") == 0)
|
1246
|
+
filetype = RAW;
|
1247
|
+
else if (strcmp(argv[argIndex], "-raw.gz") == 0)
|
1248
|
+
filetype = RAW_GZ;
|
1249
|
+
else if (strcmp(argv[argIndex], "-fmtAuto") == 0)
|
1250
|
+
filetype = AUTO;
|
1251
|
+
else if (strcmp(argv[argIndex], "-short") == 0)
|
1252
|
+
cat = 0;
|
1253
|
+
else if (strcmp(argv[argIndex], "-shortPaired") ==
|
1254
|
+
0)
|
1255
|
+
cat = 1;
|
1256
|
+
else if (strncmp
|
1257
|
+
(argv[argIndex], "-shortPaired",
|
1258
|
+
12) == 0) {
|
1259
|
+
sscanf(argv[argIndex], "-shortPaired%hd", &short_var);
|
1260
|
+
cat = (Category) short_var;
|
1261
|
+
if (cat < 1 || cat > CATEGORIES) {
|
1262
|
+
velvetLog("Unknown option: %s\n",
|
1263
|
+
argv[argIndex]);
|
1264
|
+
#ifdef DEBUG
|
1265
|
+
abort();
|
1266
|
+
#endif
|
1267
|
+
exit(1);
|
1268
|
+
}
|
1269
|
+
cat--;
|
1270
|
+
cat *= 2;
|
1271
|
+
cat++;
|
1272
|
+
} else if (strncmp(argv[argIndex], "-short", 6) ==
|
1273
|
+
0) {
|
1274
|
+
sscanf(argv[argIndex], "-short%hd", &short_var);
|
1275
|
+
cat = (Category) short_var;
|
1276
|
+
if (cat < 1 || cat > CATEGORIES) {
|
1277
|
+
velvetLog("Unknown option: %s\n",
|
1278
|
+
argv[argIndex]);
|
1279
|
+
#ifdef DEBUG
|
1280
|
+
abort();
|
1281
|
+
#endif
|
1282
|
+
exit(1);
|
1283
|
+
}
|
1284
|
+
cat--;
|
1285
|
+
cat *= 2;
|
1286
|
+
} else if (strcmp(argv[argIndex], "-long") == 0)
|
1287
|
+
cat = LONG; // CATEGORIES * 2;
|
1288
|
+
else if (strcmp(argv[argIndex], "-longPaired") == 0)
|
1289
|
+
cat = LONG_PAIRED; // CATEGORIES * 2 + 1;
|
1290
|
+
else if (strcmp(argv[argIndex], "-reference") == 0)
|
1291
|
+
cat = REFERENCE; // CATEGORIES * 2 + 2
|
1292
|
+
else if (strcmp(argv[argIndex], "-strand_specific") == 0) {
|
1293
|
+
*double_strand = false;
|
1294
|
+
reference_coordinate_double_strand = false;
|
1295
|
+
} else if (strcmp(argv[argIndex], "-noHash") == 0) {
|
1296
|
+
;
|
1297
|
+
} else if (strcmp(argv[argIndex], "-create_binary") == 0) {
|
1298
|
+
;
|
1299
|
+
} else if (strcmp(argv[argIndex], "-interleaved") == 0) {
|
1300
|
+
separate_pair_files = false;
|
1301
|
+
} else if (strcmp(argv[argIndex], "-separate") == 0) {
|
1302
|
+
separate_pair_files = true;
|
1303
|
+
}
|
1304
|
+
else {
|
1305
|
+
velvetLog("Unknown option: %s\n",
|
1306
|
+
argv[argIndex]);
|
1307
|
+
#ifdef DEBUG
|
1308
|
+
abort();
|
1309
|
+
#endif
|
1310
|
+
exit(1);
|
1311
|
+
}
|
1312
|
+
|
1313
|
+
continue;
|
1314
|
+
}
|
1315
|
+
|
1316
|
+
if (cat == -1)
|
1317
|
+
continue;
|
1318
|
+
|
1319
|
+
switch (filetype) {
|
1320
|
+
case FASTA:
|
1321
|
+
case FASTQ:
|
1322
|
+
case FASTA_GZ:
|
1323
|
+
case FASTQ_GZ:
|
1324
|
+
case AUTO:
|
1325
|
+
// Separate files for paired reads? Note odd categories used for paired read type
|
1326
|
+
if (separate_pair_files && cat%2==1) {
|
1327
|
+
argIndex++;
|
1328
|
+
if (argIndex>=argc)
|
1329
|
+
exitErrorf(EXIT_FAILURE, false, "Require left & right filename for -separate mode");
|
1330
|
+
readFastXPair(filetype, seqWriteInfo, argv[argIndex-1], argv[argIndex], cat, &sequenceIndex);
|
1331
|
+
} else {
|
1332
|
+
readFastXFile(filetype, seqWriteInfo, argv[argIndex], cat, &sequenceIndex, refCoords);
|
1333
|
+
}
|
1334
|
+
break;
|
1335
|
+
case RAW:
|
1336
|
+
if (separate_pair_files && cat%2==1) {
|
1337
|
+
exitErrorf(EXIT_FAILURE, false, "Currently do not support -separate mode for RAW");
|
1338
|
+
}
|
1339
|
+
readRawFile(seqWriteInfo, argv[argIndex], cat, &sequenceIndex);
|
1340
|
+
break;
|
1341
|
+
case RAW_GZ:
|
1342
|
+
if (separate_pair_files && cat%2==1) {
|
1343
|
+
exitErrorf(EXIT_FAILURE, false, "Currently do not support -separate mode for RAW");
|
1344
|
+
}
|
1345
|
+
readRawGZFile(seqWriteInfo, argv[argIndex], cat, &sequenceIndex);
|
1346
|
+
break;
|
1347
|
+
case SAM:
|
1348
|
+
readSAMFile(seqWriteInfo, argv[argIndex], cat, &sequenceIndex, refCoords);
|
1349
|
+
break;
|
1350
|
+
case BAM:
|
1351
|
+
readBAMFile(seqWriteInfo, argv[argIndex], cat, &sequenceIndex, refCoords);
|
1352
|
+
break;
|
1353
|
+
default:
|
1354
|
+
velvetLog("Screw up in parser... exiting\n");
|
1355
|
+
#ifdef DEBUG
|
1356
|
+
abort();
|
1357
|
+
#endif
|
1358
|
+
exit(1);
|
1359
|
+
}
|
1360
|
+
}
|
1361
|
+
|
1362
|
+
destroyReferenceCoordinateTable(refCoords);
|
1363
|
+
if (isCreateBinary()) {
|
1364
|
+
closeCnySeqForWrite(seqWriteInfo);
|
1365
|
+
} else {
|
1366
|
+
fclose(seqWriteInfo->m_pFile);
|
1367
|
+
}
|
1368
|
+
if (seqWriteInfo) {
|
1369
|
+
free(seqWriteInfo);
|
1370
|
+
}
|
1371
|
+
}
|
1372
|
+
|
1373
|
+
void createReadPairingArray(ReadSet* reads)
|
1374
|
+
{
|
1375
|
+
IDnum index;
|
1376
|
+
IDnum *mateReads = mallocOrExit(reads->readCount, IDnum);
|
1377
|
+
Category cat = 0;
|
1378
|
+
int phase = 0;
|
1379
|
+
|
1380
|
+
for (index = 0; index < reads->readCount; index++)
|
1381
|
+
mateReads[index] = -1;
|
1382
|
+
|
1383
|
+
reads->mateReads = mateReads;
|
1384
|
+
|
1385
|
+
for (index = 0; index < reads->readCount; index++)
|
1386
|
+
{
|
1387
|
+
// Paired category
|
1388
|
+
if (cat & 1)
|
1389
|
+
{
|
1390
|
+
// Leaving the paired category
|
1391
|
+
if (reads->categories[index] != cat)
|
1392
|
+
{
|
1393
|
+
if (phase == 1)
|
1394
|
+
{
|
1395
|
+
reads->mateReads[index - 1] = -1;
|
1396
|
+
reads->categories[index - 1]--;
|
1397
|
+
phase = 0;
|
1398
|
+
}
|
1399
|
+
cat = reads->categories[index];
|
1400
|
+
// Into another paired category
|
1401
|
+
if (cat & 1)
|
1402
|
+
{
|
1403
|
+
reads->mateReads[index] = index + 1;
|
1404
|
+
phase = 1;
|
1405
|
+
}
|
1406
|
+
}
|
1407
|
+
else if (phase == 0)
|
1408
|
+
{
|
1409
|
+
reads->mateReads[index] = index + 1;
|
1410
|
+
phase = 1;
|
1411
|
+
}
|
1412
|
+
else
|
1413
|
+
{
|
1414
|
+
reads->mateReads[index] = index - 1;
|
1415
|
+
phase = 0;
|
1416
|
+
}
|
1417
|
+
}
|
1418
|
+
// Leaving an unpaired category
|
1419
|
+
else if (reads->categories[index] != cat)
|
1420
|
+
{
|
1421
|
+
cat = reads->categories[index];
|
1422
|
+
// Into a paired category
|
1423
|
+
if (cat & 1)
|
1424
|
+
{
|
1425
|
+
reads->mateReads[index] = index + 1;
|
1426
|
+
phase = 1;
|
1427
|
+
}
|
1428
|
+
}
|
1429
|
+
}
|
1430
|
+
}
|
1431
|
+
|
1432
|
+
int pairedCategories(ReadSet * reads)
|
1433
|
+
{
|
1434
|
+
boolean pairedCat[CATEGORIES + 1];
|
1435
|
+
int pairedCatCount = 0;
|
1436
|
+
IDnum index;
|
1437
|
+
|
1438
|
+
for (index = 0; index <= CATEGORIES; index++)
|
1439
|
+
pairedCat[index] = 0;
|
1440
|
+
|
1441
|
+
for (index = 0; index < reads->readCount; index++) {
|
1442
|
+
if (reads->categories[index] & 1 && !pairedCat[reads->categories[index] / 2]) {
|
1443
|
+
pairedCat[reads->categories[index] / 2] = true;
|
1444
|
+
if (pairedCatCount++ == CATEGORIES)
|
1445
|
+
break;
|
1446
|
+
}
|
1447
|
+
}
|
1448
|
+
|
1449
|
+
return pairedCatCount;
|
1450
|
+
}
|
1451
|
+
|
1452
|
+
boolean isSecondInPair(ReadSet * reads, IDnum index)
|
1453
|
+
{
|
1454
|
+
return reads->secondInPair[index / 8] & (1 << (index & 7));
|
1455
|
+
}
|
1456
|
+
|
1457
|
+
void computeSecondInPair(ReadSet * reads)
|
1458
|
+
{
|
1459
|
+
IDnum index;
|
1460
|
+
Category currentCat = 0;
|
1461
|
+
Category previousCat = 0;
|
1462
|
+
int phase = 0;
|
1463
|
+
|
1464
|
+
if (reads->secondInPair)
|
1465
|
+
free (reads->secondInPair);
|
1466
|
+
reads->secondInPair = callocOrExit((reads->readCount + 7) / 8, unsigned char);
|
1467
|
+
|
1468
|
+
for (index = 0; index < reads->readCount; index++)
|
1469
|
+
{
|
1470
|
+
currentCat = reads->categories[index];
|
1471
|
+
if (currentCat & 1)
|
1472
|
+
{
|
1473
|
+
if (previousCat == currentCat)
|
1474
|
+
{
|
1475
|
+
if (phase == 0)
|
1476
|
+
{
|
1477
|
+
phase = 1;
|
1478
|
+
}
|
1479
|
+
else
|
1480
|
+
{
|
1481
|
+
reads->secondInPair[index / 8] |= (1 << (index & 7));
|
1482
|
+
phase = 0;
|
1483
|
+
}
|
1484
|
+
}
|
1485
|
+
else {
|
1486
|
+
phase = 1;
|
1487
|
+
if (index > 0 && previousCat & 1 && !isSecondInPair(reads, index - 1))
|
1488
|
+
reads->categories[index - 1] = (reads->categories[index - 1] / 2) * 2;
|
1489
|
+
}
|
1490
|
+
}
|
1491
|
+
previousCat = currentCat;
|
1492
|
+
}
|
1493
|
+
|
1494
|
+
// Safeguard against odd sets of reads
|
1495
|
+
if (!isSecondInPair(reads, reads->readCount - 1)) {
|
1496
|
+
reads->categories[reads->readCount - 1] = (reads->categories[reads->readCount - 1] / 2) * 2;
|
1497
|
+
}
|
1498
|
+
}
|
1499
|
+
|
1500
|
+
void detachDubiousReads(ReadSet * reads, boolean * dubiousReads)
|
1501
|
+
{
|
1502
|
+
IDnum index;
|
1503
|
+
IDnum pairID;
|
1504
|
+
IDnum sequenceCount = reads->readCount;
|
1505
|
+
IDnum *mateReads = reads->mateReads;
|
1506
|
+
|
1507
|
+
if (dubiousReads == NULL || mateReads == NULL)
|
1508
|
+
return;
|
1509
|
+
|
1510
|
+
for (index = 0; index < sequenceCount; index++) {
|
1511
|
+
if (!dubiousReads[index] || reads->categories[index] % 2 == 0 )
|
1512
|
+
continue;
|
1513
|
+
|
1514
|
+
if (isSecondInPair(reads, index))
|
1515
|
+
pairID = index - 1;
|
1516
|
+
else
|
1517
|
+
pairID = index + 1;
|
1518
|
+
|
1519
|
+
reads->categories[index] = (reads->categories[index] / 2) * 2;
|
1520
|
+
reads->categories[pairID] = (reads->categories[pairID] / 2) * 2;
|
1521
|
+
}
|
1522
|
+
}
|
1523
|
+
|
1524
|
+
ReadSet *importReadSet(char *filename)
|
1525
|
+
{
|
1526
|
+
FILE *file = fopen(filename, "r");
|
1527
|
+
char *sequence = NULL;
|
1528
|
+
Coordinate bpCount = 0;
|
1529
|
+
const int maxline = 5000;
|
1530
|
+
char line[5000];
|
1531
|
+
IDnum sequenceCount, sequenceIndex;
|
1532
|
+
ReadSet *reads;
|
1533
|
+
short int temp_short;
|
1534
|
+
int lineLength;
|
1535
|
+
|
1536
|
+
if (file != NULL)
|
1537
|
+
velvetLog("Reading read set file %s;\n", filename);
|
1538
|
+
else
|
1539
|
+
exitErrorf(EXIT_FAILURE, true, "Could not open %s", filename);
|
1540
|
+
|
1541
|
+
reads = newReadSet();
|
1542
|
+
|
1543
|
+
// Count number of separate sequences
|
1544
|
+
sequenceCount = 0;
|
1545
|
+
while (fgets(line, maxline, file) != NULL)
|
1546
|
+
if (line[0] == '>')
|
1547
|
+
sequenceCount++;
|
1548
|
+
fclose(file);
|
1549
|
+
velvetLog("%li sequences found\n", (long) sequenceCount);
|
1550
|
+
|
1551
|
+
reads->readCount = sequenceCount;
|
1552
|
+
|
1553
|
+
if (reads->readCount == 0) {
|
1554
|
+
reads->sequences = NULL;
|
1555
|
+
reads->categories = NULL;
|
1556
|
+
return reads;
|
1557
|
+
}
|
1558
|
+
|
1559
|
+
reads->sequences = callocOrExit(sequenceCount, char *);
|
1560
|
+
reads->categories = callocOrExit(sequenceCount, Category);
|
1561
|
+
// Counting base pair length of each sequence:
|
1562
|
+
file = fopen(filename, "r");
|
1563
|
+
sequenceIndex = -1;
|
1564
|
+
while (fgets(line, maxline, file) != NULL) {
|
1565
|
+
if (line[0] == '>') {
|
1566
|
+
|
1567
|
+
// Reading category info
|
1568
|
+
sscanf(line, "%*[^\t]\t%*[^\t]\t%hd",
|
1569
|
+
&temp_short);
|
1570
|
+
reads->categories[sequenceIndex + 1] = (Category) temp_short;
|
1571
|
+
|
1572
|
+
if (sequenceIndex != -1)
|
1573
|
+
reads->sequences[sequenceIndex] =
|
1574
|
+
mallocOrExit(bpCount + 1, char);
|
1575
|
+
sequenceIndex++;
|
1576
|
+
bpCount = 0;
|
1577
|
+
} if (line[0] == 'M') {;
|
1578
|
+
// Map line
|
1579
|
+
} else {
|
1580
|
+
bpCount += (Coordinate) strlen(line) - 1;
|
1581
|
+
|
1582
|
+
if (sizeof(ShortLength) == sizeof(int16_t) && (bpCount > SHRT_MAX || bpCount < 0)) {
|
1583
|
+
velvetLog("Read %li of length %lli, longer than limit %i\n",
|
1584
|
+
(long) sequenceIndex + 1, (long long) bpCount, SHRT_MAX);
|
1585
|
+
velvetLog("You should modify recompile with the LONGSEQUENCES option (cf. manual)\n");
|
1586
|
+
exit(1);
|
1587
|
+
}
|
1588
|
+
}
|
1589
|
+
}
|
1590
|
+
|
1591
|
+
//velvetLog("Sequence %d has length %d\n", sequenceIndex, bpCount);
|
1592
|
+
reads->sequences[sequenceIndex] =
|
1593
|
+
mallocOrExit(bpCount + 1, char);
|
1594
|
+
fclose(file);
|
1595
|
+
|
1596
|
+
// Reopen file and memorize line:
|
1597
|
+
file = fopen(filename, "r");
|
1598
|
+
sequenceIndex = -1;
|
1599
|
+
while (fgets(line, maxline, file)) {
|
1600
|
+
if (line[0] == '>') {
|
1601
|
+
if (sequenceIndex != -1) {
|
1602
|
+
sequence[bpCount] = '\0';
|
1603
|
+
}
|
1604
|
+
sequenceIndex++;
|
1605
|
+
bpCount = 0;
|
1606
|
+
//velvetLog("Starting to read sequence %d\n",
|
1607
|
+
// sequenceIndex);
|
1608
|
+
sequence = reads->sequences[sequenceIndex];
|
1609
|
+
} else if (line[0] == 'M') {;
|
1610
|
+
// Map line
|
1611
|
+
} else {
|
1612
|
+
lineLength = strlen(line) - 1;
|
1613
|
+
strncpy(sequence + bpCount, line, lineLength);
|
1614
|
+
bpCount += (Coordinate) lineLength;
|
1615
|
+
}
|
1616
|
+
}
|
1617
|
+
|
1618
|
+
sequence[bpCount] = '\0';
|
1619
|
+
fclose(file);
|
1620
|
+
computeSecondInPair(reads);
|
1621
|
+
|
1622
|
+
velvetLog("Done\n");
|
1623
|
+
return reads;
|
1624
|
+
|
1625
|
+
}
|
1626
|
+
|
1627
|
+
void logInstructions(int argc, char **argv, char *directory)
|
1628
|
+
{
|
1629
|
+
int index;
|
1630
|
+
char *logFilename =
|
1631
|
+
mallocOrExit(strlen(directory) + 100, char);
|
1632
|
+
FILE *logFile;
|
1633
|
+
time_t date;
|
1634
|
+
char *string;
|
1635
|
+
|
1636
|
+
time(&date);
|
1637
|
+
string = ctime(&date);
|
1638
|
+
|
1639
|
+
strcpy(logFilename, directory);
|
1640
|
+
strcat(logFilename, "/Log");
|
1641
|
+
logFile = fopen(logFilename, "a");
|
1642
|
+
|
1643
|
+
if (logFile == NULL)
|
1644
|
+
exitErrorf(EXIT_FAILURE, true, "Could not write to %s", logFilename);
|
1645
|
+
|
1646
|
+
velvetFprintf(logFile, "%s", string);
|
1647
|
+
|
1648
|
+
for (index = 0; index < argc; index++)
|
1649
|
+
velvetFprintf(logFile, " %s", argv[index]);
|
1650
|
+
|
1651
|
+
velvetFprintf(logFile, "\n");
|
1652
|
+
|
1653
|
+
velvetFprintf(logFile, "Version %i.%i.%2.2i\n", VERSION_NUMBER,
|
1654
|
+
RELEASE_NUMBER, UPDATE_NUMBER);
|
1655
|
+
velvetFprintf(logFile, "Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)\n");
|
1656
|
+
velvetFprintf(logFile, "This is free software; see the source for copying conditions. There is NO\n");
|
1657
|
+
velvetFprintf(logFile, "warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.\n");
|
1658
|
+
velvetFprintf(logFile, "Compilation settings:\n");
|
1659
|
+
velvetFprintf(logFile, "CATEGORIES = %i\n", CATEGORIES);
|
1660
|
+
velvetFprintf(logFile, "MAXKMERLENGTH = %i\n", MAXKMERLENGTH);
|
1661
|
+
#ifdef _OPENMP
|
1662
|
+
velvetFprintf(logFile, "OPENMP\n");
|
1663
|
+
#endif
|
1664
|
+
#ifdef LONGSEQUENCES
|
1665
|
+
velvetFprintf(logFile, "LONGSEQUENCES\n");
|
1666
|
+
#endif
|
1667
|
+
#ifdef BIGASSEMBLY
|
1668
|
+
velvetFprintf(logFile, "BIGASSEMBLY\n");
|
1669
|
+
#endif
|
1670
|
+
#ifdef COLOR
|
1671
|
+
velvetFprintf(logFile, "COLOR\n");
|
1672
|
+
#endif
|
1673
|
+
#ifdef DEBUG
|
1674
|
+
velvetFprintf(logFile, "DEBUG\n");
|
1675
|
+
#endif
|
1676
|
+
velvetFprintf(logFile, "\n");
|
1677
|
+
|
1678
|
+
fclose(logFile);
|
1679
|
+
free(logFilename);
|
1680
|
+
}
|
1681
|
+
|
1682
|
+
void destroyReadSet(ReadSet * reads)
|
1683
|
+
{
|
1684
|
+
IDnum index;
|
1685
|
+
|
1686
|
+
if (reads == NULL)
|
1687
|
+
return;
|
1688
|
+
|
1689
|
+
if (reads->sequences != NULL)
|
1690
|
+
{
|
1691
|
+
for (index = 0; index < reads->readCount; index++)
|
1692
|
+
free(reads->sequences[index]);
|
1693
|
+
free(reads->sequences);
|
1694
|
+
}
|
1695
|
+
|
1696
|
+
if (reads->tSequences != NULL)
|
1697
|
+
free (reads->tSequences);
|
1698
|
+
|
1699
|
+
if (reads->tSeqMem != NULL)
|
1700
|
+
free (reads->tSeqMem);
|
1701
|
+
|
1702
|
+
if (reads->labels != NULL)
|
1703
|
+
for (index = 0; index < reads->readCount; index++)
|
1704
|
+
free(reads->labels[index]);
|
1705
|
+
|
1706
|
+
if (reads->confidenceScores != NULL)
|
1707
|
+
for (index = 0; index < reads->readCount; index++)
|
1708
|
+
free(reads->confidenceScores[index]);
|
1709
|
+
|
1710
|
+
if (reads->kmerProbabilities != NULL)
|
1711
|
+
for (index = 0; index < reads->readCount; index++)
|
1712
|
+
free(reads->kmerProbabilities[index]);
|
1713
|
+
|
1714
|
+
free(reads->labels);
|
1715
|
+
free(reads->confidenceScores);
|
1716
|
+
free(reads->kmerProbabilities);
|
1717
|
+
free(reads->mateReads);
|
1718
|
+
free(reads->categories);
|
1719
|
+
free(reads->secondInPair);
|
1720
|
+
free(reads);
|
1721
|
+
}
|
1722
|
+
|
1723
|
+
ShortLength *getSequenceLengths(ReadSet * reads, int wordLength)
|
1724
|
+
{
|
1725
|
+
ShortLength *lengths = callocOrExit(reads->readCount, ShortLength);
|
1726
|
+
IDnum index;
|
1727
|
+
int lengthOffset = wordLength - 1;
|
1728
|
+
|
1729
|
+
for (index = 0; index < reads->readCount; index++)
|
1730
|
+
lengths[index] =
|
1731
|
+
getLength(getTightStringInArray(reads->tSequences, index)) - lengthOffset;
|
1732
|
+
|
1733
|
+
return lengths;
|
1734
|
+
}
|