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