--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastx_toolkit-0.0.6/src/libfastx/fastx.h	Thu Aug 14 04:52:17 2014 -0400
@@ -0,0 +1,136 @@
+/*
+    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/>.
+*/
+#ifndef __FASTX_HEADER__
+#define __FASTX_HEADER__
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#ifndef PATH_MAX
+#include <linux/limits.h>
+#endif
+
+#define MIN_QUALITY_VALUE (-50)
+#define MAX_QUALITY_VALUE 50
+#define QUALITY_VALUES_RANGE (MAX_QUALITY_VALUE-MIN_QUALITY_VALUE)
+
+
+#ifndef MAX_SEQ_LINE_LENGTH 
+#define MAX_SEQ_LINE_LENGTH (25000)
+#endif
+
+typedef enum {
+	FASTA_ONLY=0,
+	FASTA_OR_FASTQ=1,
+	FASTQ_ONLY=2	
+} ALLOWED_INPUT_FILE_TYPES;
+
+typedef enum {
+	DISALLOW_N=0,
+	ALLOW_N=1
+} ALLOWED_INPUT_UNKNOWN_BASES;
+
+typedef enum {
+	REQUIRE_UPPERCASE=0,
+	ALLOW_LOWERCASE=1
+} ALLOWED_INPUT_CASE;
+
+typedef enum {
+	OUTPUT_FASTA=0,
+	OUTPUT_FASTQ_ASCII_QUAL=1,
+	OUTPUT_FASTQ_NUMERIC_QUAL=2,
+	OUTPUT_SAME_AS_INPUT=3
+} OUTPUT_FILE_TYPE;
+
+#pragma pack(1) 
+typedef struct 
+{
+	/* Record data - common for FASTA/FASTQ */
+	char    input_sequence_id_prefix[1];   //DON'T touch this - this hack will read the entire name into the variable 'name',
+				  //leaving the prefix ('>' or '@') in 'input_sequence_id_name'.
+	char    name[MAX_SEQ_LINE_LENGTH+1];
+	char    nucleotides[MAX_SEQ_LINE_LENGTH+1];
+	/* Record data - only for FASTQ */
+	char    input_name2_prefix[1];         //same hack as 'input_sequence_id_prefix'
+	char	name2[MAX_SEQ_LINE_LENGTH+1];
+	int	quality[MAX_SEQ_LINE_LENGTH+1];  //note: this is NOT ascii values, but numerical values
+					       //      numeric quality scores and ASCII quality scores
+					       //      are automatically converted to numbers (-15 to 40)
+
+	/* Configuration */
+	int	allow_input_filetype;	// 0 = Allow only FASTA
+	int	allow_N;		// 1 = N is valid nucleotide, 0 = only A/G/C/T are valid
+	int	allow_lowercase;	
+	int	read_fastq;		// 1 = Input is FASTQ (only if allow_input_fastq==1)
+	int	read_fastq_ascii;	// 1 = Input is FASTQ with ASCII quality scores (0 = with numeric quality scores)
+	int	write_fastq;		// 0 = Write only FASTA (regardless of input type)
+	int	write_fastq_ascii;	// 1 = Write ASCII quality scores, 0 = write numeric quality scores
+	int	compress_output;		// 1 = pass output through GZIP
+
+	int     copy_input_fastq_format_to_output ; // 1 = copy 'read_fastq_ascii' to 'write_fastq_ascii'
+						    // so that the output format is the same as the input
+
+
+	/* Internal data */
+	int	allowed_nucleotides[256];	//quick lookup table for valid input	
+	char	output_sequence_id_prefix;	// '>' or '@', depending on the requested output type
+
+	char	input_file_name[PATH_MAX];	//in linux, PATH_MAX is defined in <linux/limits.h>
+	unsigned long long input_line_number;
+	char	output_file_name[PATH_MAX];	//in linux, PATH_MAX is defined in <linux/limits.h>
+
+	size_t	num_input_sequences;
+	size_t  num_output_sequences;
+	size_t  num_input_reads;
+	size_t  num_output_reads;
+
+	FILE*	input;
+	FILE*	output;
+} FASTX ;
+
+
+void fastx_init_reader(FASTX *pFASTX, const char* filename, 
+		ALLOWED_INPUT_FILE_TYPES allowed_input_filetype,
+		ALLOWED_INPUT_UNKNOWN_BASES allow_N,
+		ALLOWED_INPUT_CASE allow_lowercase);
+
+// If the sequence identifier is collapsed (= "N-N") returns the reads_count,
+// otherwise, returns 1
+int get_reads_count(const FASTX *pFASTX);
+
+void fastx_init_writer(FASTX *pFASTX,
+		const char* filename,
+		OUTPUT_FILE_TYPE output_type,
+		int compress_output);
+	
+int fastx_read_next_record(FASTX *pFASTX);
+
+void fastx_write_record(FASTX *pFASTX);
+
+size_t num_input_sequences(const FASTX *pFASTX);
+size_t num_input_reads(const FASTX *pFASTX);
+size_t num_output_sequences(const FASTX *pFASTX);
+size_t num_output_reads(const FASTX *pFASTX);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+