|
0
|
1 /*
|
|
|
2 * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
|
|
|
3 * All rights reserved.
|
|
|
4 *
|
|
|
5 * Redistribution and use in source and binary forms, with or without modification,
|
|
|
6 * are permitted provided that the following conditions are met:
|
|
|
7 *
|
|
|
8 * Redistributions of source code must retain the above copyright notice, this list
|
|
|
9 * of conditions and the following disclaimer.
|
|
|
10 * - Redistributions in binary form must reproduce the above copyright notice, this
|
|
|
11 * list of conditions and the following disclaimer in the documentation and/or other
|
|
|
12 * materials provided with the distribution.
|
|
|
13 * - Neither the names of the University of Washington, Simon Fraser University,
|
|
|
14 * nor the names of its contributors may be
|
|
|
15 * used to endorse or promote products derived from this software without specific
|
|
|
16 * prior written permission.
|
|
|
17 *
|
|
|
18 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
|
|
|
19 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
|
|
|
20 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
|
|
|
21 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
|
|
|
22 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
|
|
|
23 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
|
|
|
24 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
|
|
|
25 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
|
|
|
26 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
|
|
|
27 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
|
|
|
28 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
|
|
|
29 */
|
|
|
30
|
|
|
31
|
|
|
32 /*
|
|
|
33 Authors:
|
|
|
34 Farhad Hormozdiari
|
|
|
35 Faraz Hach
|
|
|
36 Can Alkan
|
|
|
37 Emails:
|
|
|
38 farhadh AT uw DOT edu
|
|
|
39 fhach AT cs DOT sfu DOT ca
|
|
|
40 calkan AT uw DOT edu
|
|
|
41 */
|
|
|
42
|
|
|
43
|
|
|
44 #ifndef __READ__
|
|
|
45 #define __READ__
|
|
|
46
|
|
|
47 typedef struct
|
|
|
48 {
|
|
|
49 char *name;
|
|
|
50 char *seq;
|
|
|
51 char *rseq;
|
|
|
52 char *qual;
|
|
|
53 char *hits;
|
|
|
54 int readNumber;
|
|
|
55 short *hashValue;
|
|
|
56 short *rhashValue;
|
|
|
57 int *hashValSampleSize;
|
|
|
58 } Read;
|
|
|
59
|
|
|
60 int readAllReads(char *fileName1, char *fileName2, int compressed, unsigned char *fastq, unsigned char pe, Read **seqList, unsigned int *seqListSize);
|
|
|
61 void loadSamplingLocations(int **samplingLocs, int *samplingLocsSize);
|
|
|
62 void finalizeReads(char *fileName);
|
|
|
63 void adjustQual(Read *list, int seqCnt);
|
|
|
64
|
|
|
65 #endif
|
