HSPAux.h

/*
 *
 *    HSPAux.h
 *    Soap3(gpu)
 *
 *    Copyright (C) 2011, HKU
 *
 *    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 2
 *    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, write to the Free Software
 *    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 *
 */

#ifndef __HSP_AUXILLIARY_H__
#define __HSP_AUXILLIARY_H__

#include "global_arrays.h"

typedef struct HSPAux
{
    AlgnResultArrays * algnResultArrays;
    char isFastq; // input file format - 0: No; 1: Yes
    int dpMatchScore; // match sccore for DP
    int dpMisMatchScore; // mismatch score forDP
    int alignmentType; // alignment type
    int readType; // read type: single end or paired end
    int peMaxOutputPerRead; // maximum number of hits reported per read for paired-end alignment
    int * x0_array; // the x0 array of the soap3 result
    int * x1_array; // the x1 array of the soap3 result
    int * mismatch_array; // the min number of mismatches of the soap3 result
    int minMAPQ; // minimum value of MAPQ
    int maxMAPQ; // maximum value of MAPQ
    int bwaLikeScore; // whether bwa-like MAPQ score is reported
    int g_log_n[256]; // store the value of 4.343 * log(i), for i = 0...255;
    char * readGroup; // read group
    char * sampleName; // sample name
    char * readGrpOption; // read group option
    int maxLenReadName; // max length for read name
    int ProceedDPForTooManyHits; // whether the seed will proceed to perform DP if there are too many hits
    int singleDPcutoffThreshold;
    int isPrintMDNM;

    // the following arrays for storing the soap3 results of all unpaired reads
    void * soap3AnsArray; // the list of array ptrs
    unsigned int * sa_start; // the starting positions of SA ranges
    unsigned int * occ_start; // the starting positions of occurences
    unsigned int * sa_num; // the number of SA ranges
    unsigned int * occ_num; // the number of occurences

    // the following arrays for storing the unaligned read IDs
    // for proceeding single deep-dp on them
    void * readsIDForSingleDP; // type: UnalignedSinglesArrays
    void * allHits; // store the corresponding alignment result

} HSPAux;

#endif