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/*
Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This file is part of Velvet.
Velvet is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
Velvet is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with Velvet; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
*/
#ifndef _READSET_H_
#define _READSET_H_
struct readSet_st {
char **sequences;
TightString *tSequences;
char **labels;
char *tSeqMem;
Quality **confidenceScores;
Probability **kmerProbabilities;
IDnum *mateReads;
Category *categories;
unsigned char *secondInPair;
IDnum readCount;
};
struct mask_st {
Coordinate start;
Coordinate finish;
Mask* next;
};
ReadSet *newReadSet();
ShortLength *getSequenceLengths(ReadSet * reads, int wordLength);
void convertSequences(ReadSet * rs);
ReadSet *importReadSet(char *filename);
// The overall argument parser and file reader for the hash function
void parseDataAndReadFiles(char * filename, int argc, char **argv, boolean * double_strand, boolean * noHash);
void logInstructions(int argc, char **argv, char *directory);
// Read pairing info
void createReadPairingArray(ReadSet* reads);
int pairedCategories(ReadSet * reads);
boolean isSecondInPair(ReadSet * reads, IDnum index);
void detachDubiousReads(ReadSet * reads, boolean * dubiousReads);
void destroyReadSet(ReadSet * reads);
boolean isCreateBinary();
void setCreateBinary(boolean val);
#endif
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