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comparison mrfast-2.1.0.5/Reads.h @ 1:d4054b05b015 default tip

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Version update to 2.1.0.5
author calkan
date Fri, 09 Mar 2012 07:35:51 -0500
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0:7b3dc85dc7fd 1:d4054b05b015
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