Mercurial > repos > portiahollyoak > fastuniq

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty
author portiahollyoak
date Thu, 02 Jun 2016 11:34:51 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:816cb55b5a2d
1 /****************************************************************************
2 * The 'FASTQ_PAIR' structure group was used to store paired reads and
3 * qualities, including basic operation function as well.
4 *
5 * This file was written by Haibin Xu, December 2011.
6 ****************************************************************************/
7
8 #include "fastq.h"
9
10 #ifndef _FASTQ_PAIR
11 typedef struct fastq_pair
12 {
13 FASTQ_ALL *seq_left; /* the left read */
14 FASTQ_ALL *seq_right; /* the right read */
15 } FASTQ_PAIR;
16 #define _FASTQ_PAIR
17 #endif
18
19 /* create a FASTQ pair. If successful, return the point to it,
20 * otherwise, return NULL. */
21 FASTQ_PAIR *fastq_pair_create();
22
23 /* free the FASTQ pair. If successful, return 0, otherwise return 1. */
24 int fastq_pair_remove(FASTQ_PAIR *fq_pair);
25
26 /* clear the FASTQ pair. If successful, return 0, otherwise return 1. */
27 int fastq_pair_clear(FASTQ_PAIR *fq_pair);
28
29 /* load the left and right reads and qualities for FASTQ pair from file, including description
30 * (whether_append_description=1) or not (whether_append_description=0), including quality
31 * (whether_append_quality=1) or not (whether_append_quality=0). If successful, return 0,
32 * otherwise, clear FASTQ pair and return 1. */
33 int fastq_pair_scanf(FASTQ_PAIR *fq_pair, FILE *fp_left_in, FILE *fp_right_in,
34 int whether_append_description, int whether_append_quality);
35
36 /* write the pair-end reads in FASTA or FASTQ format into two output files(format='fa' or 'fq')
37 * or in FASTA format into a single output file(format="fa" and fp_out2==NULL) using the original
38 * description (serial=-1) or the new serial. If successful, return 0, otherwise, return 1. */
39 int fastq_pair_printf(FASTQ_PAIR *fq_pair, FILE *fp_out1, FILE *fp_out2,
40 char *format, long serial);
41
42 /* compare the two FASTQ pairs tightly, if identical, return 0, else if a>b,
43 * return 1, else if a<b, return -1. */
44 int fastq_pair_compare_tight(FASTQ_PAIR *fq_pair_a, FASTQ_PAIR *fq_pair_b);
45
46 /* compare the two FASTQ pairs loosely, if identical, return 0, else if a>b,
47 * return 1, else if a<b, return -1. */
48 int fastq_pair_compare_loose(FASTQ_PAIR *fq_pair_a, FASTQ_PAIR *fq_pair_b);
49
50 /* return the length of left FASTQ sequence in pair, if any error, return -1. */
51 long fastq_pair_get_left_length(FASTQ_PAIR *fq_pair);
52
53 /* return the length of right FASTQ sequence in pair, if any error, return -1. */
54 long fastq_pair_get_right_length(FASTQ_PAIR *fq_pair);
55
56 /* return the length of both left and right FASTQ sequence in pair,
57 * if any error, return -1. */
58 long fastq_pair_get_total_length(FASTQ_PAIR *fq_pair);
59
60
61