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comparison fastx_toolkit-0.0.6/src/fastq_quality_converter/fastq_quality_converter.c @ 3:997f5136985f draft default tip

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author xilinxu
date Thu, 14 Aug 2014 04:52:17 -0400
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2:dfe9332138cf 3:997f5136985f
1 /*
2 FASTX-toolkit - FASTA/FASTQ preprocessing tools.
3 Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
4
5 This program is free software: you can redistribute it and/or modify
6 it under the terms of the GNU Affero General Public License as
7 published by the Free Software Foundation, either version 3 of the
8 License, or (at your option) any later version.
9
10 This program is distributed in the hope that it will be useful,
11 but WITHOUT ANY WARRANTY; without even the implied warranty of
12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 GNU Affero General Public License for more details.
14
15 You should have received a copy of the GNU Affero General Public License
16 along with this program. If not, see <http://www.gnu.org/licenses/>.
17 */
18 #include <limits.h>
19 #include <stdio.h>
20 #include <stdlib.h>
21 #include <string.h>
22 #include <getopt.h>
23 #include <errno.h>
24 #include <err.h>
25
26 #include <config.h>
27
28 #include "fastx.h"
29 #include "fastx_args.h"
30
31 const char* usage=
32 "usage: fastq_quality_converter [-h] [-a] [-n] [-z] [-i INFILE] [-f OUTFILE]\n" \
33 "\n" \
34 "version " VERSION "\n" \
35 " [-h] = This helpful help screen.\n" \
36 " [-a] = Output ASCII quality scores (default).\n" \
37 " [-n] = Output numeric quality scores.\n" \
38 " [-z] = Compress output with GZIP.\n" \
39 " [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \
40 " [-o OUTFILE] = FASTA output file. default is STDOUT.\n" \
41 "\n";
42
43 FASTX fastx;
44 int flag_output_ascii = 1;
45
46 int parse_program_args(int __attribute__((unused)) optind, int optc, char __attribute__((unused)) *optarg)
47 {
48 switch(optc) {
49 case 'a': //this is the default, nothing to change
50 break;
51
52 case 'n':
53 flag_output_ascii = 0 ;
54 break;
55 default:
56 errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ;
57 }
58 return 1;
59 }
60
61
62 int main(int argc, char* argv[])
63 {
64 fastx_parse_cmdline(argc, argv, "an", parse_program_args);
65
66 fastx_init_reader(&fastx, get_input_filename(),
67 FASTQ_ONLY, ALLOW_N, REQUIRE_UPPERCASE);
68
69 fastx_init_writer(&fastx, get_output_filename(),
70 flag_output_ascii ? OUTPUT_FASTQ_ASCII_QUAL : OUTPUT_FASTQ_NUMERIC_QUAL,
71 compress_output_flag());
72
73 while ( fastx_read_next_record(&fastx) ) {
74 fastx_write_record(&fastx);
75 }
76
77 //Print verbose report
78 if ( verbose_flag() ) {
79 fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ;
80 fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ;
81 }
82 return 0;
83 }