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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' structure group was used to store paired reads and
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3 * qualities, 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.h"
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10 #ifndef _FASTQ_PAIR
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11 typedef struct fastq_pair
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12 {
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13 FASTQ_ALL *seq_left; /* the left read */
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14 FASTQ_ALL *seq_right; /* the right read */
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15 } FASTQ_PAIR;
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16 #define _FASTQ_PAIR
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17 #endif
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19 /* create a FASTQ pair. If successful, return the point to it,
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20 * otherwise, return NULL. */
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21 FASTQ_PAIR *fastq_pair_create();
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23 /* free the FASTQ pair. If successful, return 0, otherwise return 1. */
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24 int fastq_pair_remove(FASTQ_PAIR *fq_pair);
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26 /* clear the FASTQ pair. If successful, return 0, otherwise return 1. */
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27 int fastq_pair_clear(FASTQ_PAIR *fq_pair);
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29 /* load the left and right reads and qualities for FASTQ pair from file, including description
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30 * (whether_append_description=1) or not (whether_append_description=0), including quality
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31 * (whether_append_quality=1) or not (whether_append_quality=0). If successful, return 0,
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32 * otherwise, clear FASTQ pair and return 1. */
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33 int fastq_pair_scanf(FASTQ_PAIR *fq_pair, FILE *fp_left_in, FILE *fp_right_in,
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34 int whether_append_description, int whether_append_quality);
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36 /* write the pair-end reads in FASTA or FASTQ format into two output files(format='fa' or 'fq')
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37 * or in FASTA format into a single output file(format="fa" and fp_out2==NULL) using the original
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38 * description (serial=-1) or the new serial. If successful, return 0, otherwise, return 1. */
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39 int fastq_pair_printf(FASTQ_PAIR *fq_pair, FILE *fp_out1, FILE *fp_out2,
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40 char *format, long serial);
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42 /* compare the two FASTQ pairs tightly, if identical, return 0, else if a>b,
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43 * return 1, else if a<b, return -1. */
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44 int fastq_pair_compare_tight(FASTQ_PAIR *fq_pair_a, FASTQ_PAIR *fq_pair_b);
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46 /* compare the two FASTQ pairs loosely, if identical, return 0, else if a>b,
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47 * return 1, else if a<b, return -1. */
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48 int fastq_pair_compare_loose(FASTQ_PAIR *fq_pair_a, FASTQ_PAIR *fq_pair_b);
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50 /* return the length of left FASTQ sequence in pair, if any error, return -1. */
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51 long fastq_pair_get_left_length(FASTQ_PAIR *fq_pair);
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53 /* return the length of right FASTQ sequence in pair, if any error, return -1. */
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54 long fastq_pair_get_right_length(FASTQ_PAIR *fq_pair);
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56 /* return the length of both left and right FASTQ sequence in pair,
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57 * if any error, return -1. */
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58 long fastq_pair_get_total_length(FASTQ_PAIR *fq_pair);
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