Mercurial > repos > portiahollyoak > fastuniq
comparison source/fastq.h @ 0:816cb55b5a2d draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty
author | portiahollyoak |
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date | Thu, 02 Jun 2016 11:34:51 -0400 |
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1 /**************************************************************************** | |
2 * The 'FASTQ_ALL' structure group was used to store nucleotide sequence in | |
3 * fastq format, including basic operation function as well. | |
4 * | |
5 * This file was written by Haibin Xu, December 2011. | |
6 ****************************************************************************/ | |
7 | |
8 #include <stdio.h> | |
9 #include <stdlib.h> | |
10 #include <string.h> | |
11 | |
12 #ifndef FASTQ_DESCRIPTION_MAX_LENGTH | |
13 #define FASTQ_DESCRIPTION_MAX_LENGTH 1000 | |
14 #endif | |
15 | |
16 #ifndef FASTQ_SEQUENCE_MAX_LENGTH | |
17 #define FASTQ_SEQUENCE_MAX_LENGTH 2000 | |
18 #endif | |
19 | |
20 #ifndef _FASTQ_ALL | |
21 typedef struct fastq_all | |
22 { | |
23 char *description_1; /* the 1st description line */ | |
24 char *sequence; /* the sequence*/ | |
25 char *description_2; /* the 2nd description line */ | |
26 char *quality; /* the quality */ | |
27 } FASTQ_ALL; | |
28 #define _FASTQ_ALL | |
29 #endif | |
30 | |
31 /* create a FASTQ_ALL sequence. If successful, return the point to it, | |
32 * otherwise, return NULL. */ | |
33 FASTQ_ALL *fastq_create(); | |
34 | |
35 /* free the FASTQ sequence. If successful, return 0, otherwise return 1. */ | |
36 int fastq_remove(FASTQ_ALL *fq); | |
37 | |
38 /* clear the FASTQ sequence. If successful, return 0, otherwise return 1. */ | |
39 int fastq_clear(FASTQ_ALL *fq); | |
40 | |
41 /* get sequence serial from FASTQ description in format '@serial_number'. | |
42 * If successful return the serial, otherwise return -1. */ | |
43 long fastq_get_serial(FASTQ_ALL *fq); | |
44 | |
45 /* read a FASTQ sequence from input file, including description (whether_append_description=1) | |
46 * or not (whether_append_description=0), including quality (whether_append_quality=1) or not | |
47 * (whether_append_quality=0). If successful, return 0, otherwise, clear fq | |
48 * and return 1. */ | |
49 int fastq_scanf(FASTQ_ALL *fq, FILE *fp_in, | |
50 int whether_append_description, int whether_append_quality); | |
51 | |
52 /* write sequence into output file in FASTQ format(format='fq') or FASTA format(format='fa') | |
53 * using the original description (serial=-1) or the new serial. | |
54 * If successful, return 0, otherwise return 1. */ | |
55 int fastq_printf(FASTQ_ALL *fq, FILE *fp_out, char *format, long serial); | |
56 | |
57 /* return the length of FASTQ sequence, if any error, return -1. */ | |
58 long fastq_get_length(FASTQ_ALL *fq); | |
59 | |
60 | |
61 |