Mercurial > repos > xilinxu > xilinxu
diff fastx_toolkit-0.0.6/src/fastq_quality_converter/fastq_quality_converter.c @ 3:997f5136985f draft default tip
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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_toolkit-0.0.6/src/fastq_quality_converter/fastq_quality_converter.c Thu Aug 14 04:52:17 2014 -0400 @@ -0,0 +1,83 @@ +/* + FASTX-toolkit - FASTA/FASTQ preprocessing tools. + Copyright (C) 2009 A. Gordon (gordon@cshl.edu) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as + published by the Free Software Foundation, either version 3 of the + License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. +*/ +#include <limits.h> +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#include <getopt.h> +#include <errno.h> +#include <err.h> + +#include <config.h> + +#include "fastx.h" +#include "fastx_args.h" + +const char* usage= +"usage: fastq_quality_converter [-h] [-a] [-n] [-z] [-i INFILE] [-f OUTFILE]\n" \ +"\n" \ +"version " VERSION "\n" \ +" [-h] = This helpful help screen.\n" \ +" [-a] = Output ASCII quality scores (default).\n" \ +" [-n] = Output numeric quality scores.\n" \ +" [-z] = Compress output with GZIP.\n" \ +" [-i INFILE] = FASTA/Q input file. default is STDIN.\n" \ +" [-o OUTFILE] = FASTA output file. default is STDOUT.\n" \ +"\n"; + +FASTX fastx; +int flag_output_ascii = 1; + +int parse_program_args(int __attribute__((unused)) optind, int optc, char __attribute__((unused)) *optarg) +{ + switch(optc) { + case 'a': //this is the default, nothing to change + break; + + case 'n': + flag_output_ascii = 0 ; + break; + default: + errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ; + } + return 1; +} + + +int main(int argc, char* argv[]) +{ + fastx_parse_cmdline(argc, argv, "an", parse_program_args); + + fastx_init_reader(&fastx, get_input_filename(), + FASTQ_ONLY, ALLOW_N, REQUIRE_UPPERCASE); + + fastx_init_writer(&fastx, get_output_filename(), + flag_output_ascii ? OUTPUT_FASTQ_ASCII_QUAL : OUTPUT_FASTQ_NUMERIC_QUAL, + compress_output_flag()); + + while ( fastx_read_next_record(&fastx) ) { + fastx_write_record(&fastx); + } + + //Print verbose report + if ( verbose_flag() ) { + fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ; + fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ; + } + return 0; +}