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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 INTSEQUENCE_H
#define INTSEQUENCE_H
/*
* charsequence.h
* declaration of char sequence
* and functions working on it
*
* @author Steve Hoffmann
* @date Mon 27 Nov 2006
*
* SVN
* Revision of last commit: $Rev: 87 $
* Author: $Author: steve $
* Date: $Date: 2008-11-20 11:24:26 +0100 (Thu, 20 Nov 2008) $
*
* Id: $Id: charsequence.h 87 2008-11-20 10:24:26Z steve $
* Url: $URL: http://www.bioinf.uni-leipzig.de/svn/segemehl/segemehl/branches/esa/trunk/libs/sufarray/charsequence.h $
*/
#include "basic-types.h"
#include <stdio.h>
#include <stdlib.h>
#include "stringutils.h"
typedef struct {
Uint descrlen;
Uint namelen;
Uint urllen;
Uint noofinfo;
Uint *infolength;
char *description; /*a description*/
char *alphabetname; /*the name of the corresponding alphabet*/
char *url; /*the name of the sequences url*/
char *sequence; /*the sequence itself*/
char *info; /*additional information*/
Uint length;
Uint clip5[2]; /*clipping information*/
Uint clip3[2];
#ifdef HASHING
Uint quantity; /* quantity of equal sequences */
#endif
Uint *map;
Uint mapsize;
} CharSequence;
void destructSequence(void *, CharSequence *);
CharSequence* initSequence(void *);
void resetSequence(CharSequence *);
char* printSequence(void *, CharSequence *, Uint);
void dumpSequence(CharSequence *s);
void saveSequence (CharSequence *s, char *filename);
CharSequence* loadSequence (void *space, char *filename);
char * printAlignment (void *, int *, Uint, CharSequence *, CharSequence *,
Uint);
CharSequence** createSequenceHash(void *, Uint);
static inline char* charDNAcomplement(void *space, char *s, Uint len) {
Uint i,k=0;
char* buffer;
buffer = ALLOCMEMORY(space, NULL, char, len+1);
for(i=len; i > 0; i--) {
switch(s[i-1]) {
case 'a':
buffer[k] = 't';
break;
case 't':
buffer[k] = 'a';
break;
case 'c':
buffer[k] = 'g';
break;
case 'g':
buffer[k] = 'c';
break;
case 'n':
buffer[k] = 'n';
break;
case 'A':
buffer[k] = 'T';
break;
case 'T':
buffer[k] = 'A';
break;
case 'C':
buffer[k] = 'G';
break;
case 'G':
buffer[k] = 'C';
break;
case 'N':
buffer[k] = 'N';
break;
default:
buffer[k] = s[i-1];
break;
}
k++;
}
buffer[k] = '\0';
return buffer;
}
static inline char charComplementChar(char ch) {
switch(ch) {
case 'a':
return 't';
break;
case 't':
return 'a';
break;
case 'c':
return 'g';
break;
case 'g':
return 'c';
break;
case 'n':
return 'n';
break;
case 'A':
return 'T';
break;
case 'T':
return 'A';
break;
case 'C':
return 'G';
break;
case 'G':
return 'C';
break;
case 'N':
return 'N';
break;
default:
return ch;
break;
}
return ch;
}
static inline char* charIUPACcomplement(void *space, char *s, Uint len) {
Uint i,k=0;
char* buffer;
buffer = ALLOCMEMORY(space, NULL, char, len+1);
for(i=len; i > 0; i--) {
switch(s[i-1]) {
case 'a':
buffer[k] = 't';
break;
case 't':
buffer[k] = 'a';
break;
case 'c':
buffer[k] = 'g';
break;
case 'g':
buffer[k] = 'c';
break;
case 'r':
buffer[k] = 'y';
break;
case 'y':
buffer[k] = 'r';
break;
case 's':
buffer[k] = 's';
break;
case 'w':
buffer[k] = 'w';
break;
case 'k':
buffer[k] = 'm';
break;
case 'm':
buffer[k] = 'k';
break;
case 'b':
buffer[k] = 'v';
break;
case 'd':
buffer[k] = 'h';
break;
case 'h':
buffer[k] = 'd';
break;
case 'v':
buffer[k] = 'b';
break;
case 'n':
buffer[k] = 'n';
break;
case 'A':
buffer[k] = 'T';
break;
case 'T':
buffer[k] = 'A';
break;
case 'C':
buffer[k] = 'G';
break;
case 'G':
buffer[k] = 'C';
break;
case 'R':
buffer[k] = 'Y';
break;
case 'Y':
buffer[k] = 'R';
break;
case 'S':
buffer[k] = 'S';
break;
case 'W':
buffer[k] = 'W';
break;
case 'K':
buffer[k] = 'M';
break;
case 'M':
buffer[k] = 'K';
break;
case 'B':
buffer[k] = 'V';
break;
case 'D':
buffer[k] = 'H';
break;
case 'H':
buffer[k] = 'D';
break;
case 'V':
buffer[k] = 'B';
break;
case 'N':
buffer[k] = 'N';
break;
default:
buffer[k] = s[i-1];
break;
}
k++;
}
buffer[k] = '\0';
return buffer;
}
static inline void bl_convertBisulfite(char *seq, Uint len, Uint bisulfite, Uint seed) {
if (seed){
/* bisulfite or PARCLIP in run 1 */
if (bisulfite <=4 && bisulfite % 2 == 1){
//fprintf(stderr,"seed conv of reads: C --> T\n");
strconvert(seq, len, 'C', 'T');
}
/* bisulfite or PARCLIP in run 2 */
if (bisulfite <=4 && bisulfite % 2 == 0){
//fprintf(stderr,"seed conv of reads: G --> A\n");
strconvert(seq, len, 'G', 'A');
}
}
else {
/* bisulfite or PARCLIP with 4SG in run 1 */
if (bisulfite == 1){
//fprintf(stderr,"align conv of reads: T --> Y\n");
strconvert(seq, len, 'T', 'Y');
}
/* bisulfite or PARCLIP with 4SG in run 2 */
if (bisulfite == 2){
//fprintf(stderr,"align conv of reads: A --> R\n");
strconvert(seq, len, 'A', 'R');
}
/* PARCLIP with 4SU in run 1 */
if (bisulfite == 3 || bisulfite == 5){
//fprintf(stderr,"align conv of reads: C --> Y\n");
strconvert(seq, len, 'C', 'Y');
}
/* PARCLIP with 4SU in run 2 */
if (bisulfite == 4 || bisulfite == 6){
//fprintf(stderr,"align conv of reads: G --> R\n");
strconvert(seq, len, 'G', 'R');
}
}
}
static inline void bl_reconvertBisulfite(char *seq, Uint len, Uint bisulfite) {
/*
* restoring original state is only possible in case of seed == 0
* (collapsing the alphabet is unrecoverable)
* => hence seed parameter omitted here
*/
/* bisulfite or PARCLIP with 4SG in run 1 */
if (bisulfite == 1){
strconvert(seq, len, 'Y', 'T');
}
/* bisulfite or PARCLIP with 4SG in run 2 */
if (bisulfite == 2){
strconvert(seq, len, 'R', 'A');
}
/* PARCLIP with 4SU in run 1 */
if (bisulfite == 3 || bisulfite == 5){
strconvert(seq, len, 'Y', 'C');
}
/* PARCLIP with 4SU in run 2 */
if (bisulfite == 4 || bisulfite == 6){
strconvert(seq, len, 'R', 'G');
}
}
#endif
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