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comparison source/fastq_pair_array.h @ 0:816cb55b5a2d draft default tip

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planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty
author portiahollyoak
date Thu, 02 Jun 2016 11:34:51 -0400
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-1:000000000000 0:816cb55b5a2d
1 /****************************************************************************
2 * The 'FASTQ_PAIR_ARRAY' structure group was used to store a array of
3 * paired FASTQ reads, including basic operation function as well.
4 *
5 * This file was written by Haibin Xu, December 2011.
6 ****************************************************************************/
7
8 #include "fastq_pair.h"
9
10 #ifndef FASTQ_PAIR_ARRAY_BLOCK_SIZE
11 #define FASTQ_PAIR_ARRAY_BLOCK_SIZE 100000
12 #endif
13
14 #ifndef _FASTQ_PAIR_ARRAY_BLOCK
15 typedef struct fastq_pair_array_block
16 {
17 FASTQ_PAIR *block[FASTQ_PAIR_ARRAY_BLOCK_SIZE];
18 struct fastq_pair_array_block *previous;
19 struct fastq_pair_array_block *next;
20 long num;
21 } FASTQ_PAIR_ARRAY_BLOCK;
22 #define _FASTQ_PAIR_ARRAY_BLOCK
23 #endif
24
25 #ifndef _FASTQ_PAIR_ARRAY
26 typedef struct fastq_pair_array
27 {
28 FASTQ_PAIR_ARRAY_BLOCK *array;
29 FASTQ_PAIR_ARRAY_BLOCK *last;
30 long block_num;
31 long fastq_pair_num;
32 FASTQ_PAIR_ARRAY_BLOCK **index;
33 } FASTQ_PAIR_ARRAY;
34 #define _FASTQ_PAIR_ARRAY
35 #endif
36
37 /* create a FASTQ pair array. If successful, return the point to it,
38 * otherwise, return NULL. */
39 FASTQ_PAIR_ARRAY *fastq_pair_array_create();
40
41 /* free the FASTQ pair array. If successful, return 0, otherwise return 1. */
42 int fastq_pair_array_remove(FASTQ_PAIR_ARRAY *fq_pair_array);
43
44 /* append a new FASTQ pair to the array. if successful, return 0, otherwise
45 * return 1. */
46 int fastq_pair_array_append(FASTQ_PAIR *fq_pair,
47 FASTQ_PAIR_ARRAY *fq_pair_array);
48
49 /* generate the index for given FASTQ_PAIR, if successful, return 0, otherwise
50 * return 1. */
51 int fastq_pair_array_generate_index(FASTQ_PAIR_ARRAY *fq_pair_array);
52
53 /* get double pointer to individual fastq_pair member at specific position
54 * in the array, if successful, return the double pointer, otherwise
55 * return NULL */
56 FASTQ_PAIR **fastq_pair_array_get_pointer(FASTQ_PAIR_ARRAY *fq_pair_array,
57 long position);
58
59 /* merge the two sorted part in array, low-middle and middle-high, into a
60 * single sorted order. If successful, return 0, otherwise return. */
61 int fastq_pair_array_merge(FASTQ_PAIR_ARRAY *fq_pair_array,
62 FASTQ_PAIR_ARRAY *temp_fq_pair_array,
63 long low, long middle, long high);
64
65 /* sort the FASTQ pair array. If successful, return 0, otherwise
66 * return 1. */
67 int fastq_pair_array_sort(FASTQ_PAIR_ARRAY *fq_pair_array,
68 FASTQ_PAIR_ARRAY *temp_fq_pair_array,
69 long first, long last);
70
71 /* write the pair-end reads in the array in FASTA or FASTQ format into two
72 * output files(format='fa' or 'fq') or in FASTA format into a single output
73 * file(format="fa" and fp_out2==NULL) using the original description
74 * (serial_flag=0) or a new serial number(serial_flag=1). Output all sequences
75 * (flag_uniq==0), or unique ones(flag_uniq==1). If successful, return 0,
76 * otherwise return 1. */
77 int fastq_pair_array_printf(FASTQ_PAIR_ARRAY *fq_pair_array, FILE *fp_out1,
78 FILE *fp_out2, char *format, int serial_flag,
79 int flag_uniq);
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