--- /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;
+}