diff source/fastq.h @ 0:816cb55b5a2d draft default tip

planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/source/fastq.h	Thu Jun 02 11:34:51 2016 -0400
@@ -0,0 +1,61 @@
+/****************************************************************************
+ * The 'FASTQ_ALL' structure group was used to store nucleotide sequence in
+ * fastq format, including basic operation function as well.
+ *
+ * This file was written by Haibin Xu, December 2011.
+ ****************************************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#ifndef FASTQ_DESCRIPTION_MAX_LENGTH
+	#define FASTQ_DESCRIPTION_MAX_LENGTH 1000
+#endif
+
+#ifndef FASTQ_SEQUENCE_MAX_LENGTH
+	#define FASTQ_SEQUENCE_MAX_LENGTH 2000
+#endif
+
+#ifndef _FASTQ_ALL
+	typedef struct fastq_all
+		{
+			char *description_1; /* the 1st description line */
+			char *sequence; /* the sequence*/
+			char *description_2; /* the 2nd description line */
+			char *quality; /* the quality */
+		} FASTQ_ALL;
+	#define _FASTQ_ALL
+#endif
+
+/* create a FASTQ_ALL sequence. If successful, return the point to it, 
+ * otherwise, return NULL. */
+FASTQ_ALL *fastq_create();
+
+/* free the FASTQ sequence. If successful, return 0, otherwise return 1. */
+int fastq_remove(FASTQ_ALL *fq);
+
+/* clear the FASTQ sequence. If successful, return 0, otherwise return 1. */
+int fastq_clear(FASTQ_ALL *fq);
+
+/* get sequence serial from FASTQ description in format '@serial_number'. 
+ * If successful return the serial, otherwise return -1. */
+long fastq_get_serial(FASTQ_ALL *fq);
+
+/* read a FASTQ sequence from input file, including description (whether_append_description=1)
+ * or not (whether_append_description=0), including quality (whether_append_quality=1) or not
+ * (whether_append_quality=0). If successful, return 0, otherwise, clear fq
+ * and return 1. */
+int fastq_scanf(FASTQ_ALL *fq, FILE *fp_in, 
+				int whether_append_description, int whether_append_quality);
+
+/* write sequence into output file in FASTQ format(format='fq') or FASTA format(format='fa')
+ * using the original description (serial=-1) or the new serial.
+ * If successful, return 0, otherwise return 1. */
+int fastq_printf(FASTQ_ALL *fq, FILE *fp_out, char *format, long serial);
+
+/* return the length of FASTQ sequence, if any error, return -1. */
+long fastq_get_length(FASTQ_ALL *fq);
+
+
+