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/*
* segemehl - a read aligner
* Copyright (C) 2008-2017 Steve Hoffmann and Christian Otto
*
* This program 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 3 of the License, or
* (at your option) any later version.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef MULTI_SEQ_H
#define MULTI_SEQ_H
/*
* multiseq.h
* declarations for a datastructure containing
* multiple integer sequences
*
* @author Steve Hoffmann, shoffmann@zbh.uni-hamburg.de
* @company Center for Bioinformatics, Hamburg
* @date 12/11/06 15:09:15 CET
*
* SVN
* Revision of last commit: $Rev: 65 $
* Author: $Author: steve $
* Date: $Date: 2008-09-22 00:14:54 +0200 (Mon, 22 Sep 2008) $
*
* Id: $Id: multicharseq.h 65 2008-09-21 22:14:54Z steve $
* Url: $URL: http://www.bioinf.uni-leipzig.de/svn/segemehl/segemehl/branches/esa/trunk/libs/sufarray/multicharseq.h $
*/
#include "basic-types.h"
#include "charsequence.h"
#include "alignment.h"
#define MSEQ_BSEARCH_THRESHOLD 10
typedef struct {
void *ref;
} SeqReference;
typedef struct {
Uint numofsequences;
Uint totallength;
Uint *markpos; /*markpos[i] is the position of a*/
/*separator character between S_i and S_i+1*/
char *sequences; /*array of concatenated sequences*/
SeqReference *ref; /*ref[i] points to the original sequence*/
/*that starts at position markpos[i]*/
char *map;
Uint mapsize;
char delim;
} MultiCharSeq;
typedef struct {
Uint subidx;
Uint substart;
Uint subend;
char *refdesc;
char *refseq;
Uint refstart;
Uint reflen;
Uint floff;
char *qrydesc;
char *query;
char *qual;
Uint qrystart;
Uint qrylen;
Uint maxalignlen;
Alignment *al;
unsigned char strand;
unsigned char pass;
} MultiCharSeqAlignment;
void dumpMultiCharSeq (MultiCharSeq *);
MultiCharSeq* concatCharSequences(void *, CharSequence **, Uint, char, char);
void destructMultiCharSeq(void*, MultiCharSeq *);
Uint getMultiCharSeqIndex(MultiCharSeq *, char *);
Uint getMultiCharSeqRelPos(MultiCharSeq *, char *);
CharSequence* getCharSequence(MultiCharSeq *, Uint idx);
void getMultiCharSeqIdxBounds(MultiCharSeq *mseq, Uint idx, Uint *start, Uint *end);
int initMultiCharSeqAlignment(
void *space, MultiCharSeqAlignment* a, MultiCharSeq *seq, Uint pos, Uint loff, Uint len,
unsigned char strand, char *querydesc, char *query, char* qual, Uint qlen);
void wrapMultiCharSeqAlignment(void *space, MultiCharSeqAlignment *a);
int initMultiCharSeqAlignmentOpt(
void *space, MultiCharSeqAlignment* a, MultiCharSeq *seq, Uint pos,
char *qrydesc, char *query, char*qual, Uint start, Uint end,
Uint qrylen, Uint floff, Uint flen, Uint uloff, Uint uroff, Uint maxoff, unsigned char strand) ;
MultiCharSeqAlignment*
joinalignments(MultiCharSeqAlignment **al, Uint noofaligns, unsigned char rev, Uint head, Uint tail, Uint lsize, Uint rsize, Eoptype cliptype);
Uint getExtendedAlignmentLength (Uint readlength, float accuracy);
Uint getMaximumAlignmentEdist(Uint seqlength, float accuracy );
Uint bl_mcsaGet5PrimeU (MultiCharSeqAlignment *al);
Uint bl_mcsaGet3PrimeU (MultiCharSeqAlignment *al);
Uint bl_mcsaGet5primeV (MultiCharSeqAlignment *al);
MultiCharSeqAlignment* bl_getPartialMultiCharSeqAlignments (MultiCharSeqAlignment *mcsa, MultiCharSeq *mseq, Uint *noofaligns);
void reevalMultiCharSeqAlignment(MultiCharSeqAlignment *mcsa);
#endif
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