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/**********************************************************************
* Skewer - a fast and accurate adapter trimming tool
* using the bit-masked k-difference matching algorithm
* Copyright (c) 2013-2014 by Hongshan Jiang
* hongshan.jiang@gmail.com
*
* If you use this program, please cite the paper:
* Jiang, H., Lei, R., Ding, S.W. and Zhu, S. (2014) Skewer: a fast and
* accurate adapter trimmer for next-generation sequencing paired-end reads.
* BMC Bioinformatics, 15, 182.
* http://www.biomedcentral.com/1471-2105/15/182
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
#ifndef _COMMON_H
#define _COMMON_H
typedef unsigned long long uint64;
typedef unsigned long uint32;
typedef unsigned short uint16;
typedef long long int64;
typedef long int32;
typedef short int16;
#ifndef uint
typedef unsigned int uint;
#endif
typedef unsigned char uchar;
const int MAX_PATH = 255;
const int MAX_ADAPTER_LEN = 64;
const int MAX_ADAPTER_CNT = 96;
typedef struct tag_INDEX{
int pos;
int pos2;
int bc;
}INDEX;
enum TRIM_MODE{
TRIM_DEFAULT = 0,
TRIM_HEAD = 1,
TRIM_TAIL = 2,
TRIM_ANY = 3,
TRIM_PE = 4,
TRIM_PE_HEAD = 5,
TRIM_PE_TAIL = 6,
TRIM_PE_ANY = 7,
TRIM_MP = 8,
TRIM_MP_HEAD = 9,
TRIM_MP_TAIL = 10,
TRIM_MP_ANY = 11,
TRIM_AP = 16,
TRIM_AP_HEAD = 17,
TRIM_MODE_CNT = 14
};
#endif // _COMMON_H
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