diff source/fastq_pair.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_pair.h	Thu Jun 02 11:34:51 2016 -0400
@@ -0,0 +1,61 @@
+/****************************************************************************
+ * The 'FASTQ_PAIR' structure group was used to store paired reads and
+ * qualities, including basic operation function as well.
+ *
+ * This file was written by Haibin Xu, December 2011.
+ ****************************************************************************/
+
+#include "fastq.h"
+
+#ifndef _FASTQ_PAIR
+	typedef struct fastq_pair
+		{
+			FASTQ_ALL *seq_left; /* the left read */
+			FASTQ_ALL *seq_right; /* the right read */
+		} FASTQ_PAIR;
+	#define _FASTQ_PAIR
+#endif
+
+/* create a FASTQ pair. If successful, return the point to it, 
+ * otherwise, return NULL. */
+FASTQ_PAIR *fastq_pair_create();
+
+/* free the FASTQ pair. If successful, return 0, otherwise return 1. */
+int fastq_pair_remove(FASTQ_PAIR *fq_pair);
+
+/* clear the FASTQ pair. If successful, return 0, otherwise return 1. */
+int fastq_pair_clear(FASTQ_PAIR *fq_pair);
+
+/* load the left and right reads and qualities for FASTQ pair from 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 FASTQ pair and return 1. */
+int fastq_pair_scanf(FASTQ_PAIR *fq_pair, FILE *fp_left_in, FILE *fp_right_in,
+					 int whether_append_description, int whether_append_quality);
+
+/* write the pair-end reads in FASTA or FASTQ format into two output files(format='fa' or 'fq') 
+ * or in FASTA format into a single output file(format="fa" and fp_out2==NULL) using the original 
+ * description (serial=-1) or the new serial. If successful, return 0, otherwise, return 1. */
+int fastq_pair_printf(FASTQ_PAIR *fq_pair, FILE *fp_out1, FILE *fp_out2,
+					  char *format, long serial);
+
+/* compare the two FASTQ pairs tightly, if identical, return 0, else if a>b,
+ * return 1,  else if a<b, return -1. */
+int fastq_pair_compare_tight(FASTQ_PAIR *fq_pair_a, FASTQ_PAIR *fq_pair_b);
+
+/* compare the two FASTQ pairs loosely, if identical, return 0, else if a>b,
+ * return 1,  else if a<b, return -1. */
+int fastq_pair_compare_loose(FASTQ_PAIR *fq_pair_a, FASTQ_PAIR *fq_pair_b);
+
+/* return the length of left FASTQ sequence in pair, if any error, return -1. */
+long fastq_pair_get_left_length(FASTQ_PAIR *fq_pair);
+
+/* return the length of right FASTQ sequence in pair, if any error, return -1. */
+long fastq_pair_get_right_length(FASTQ_PAIR *fq_pair);
+
+/* return the length of both left and right FASTQ sequence in pair,
+ * if any error, return -1. */
+long fastq_pair_get_total_length(FASTQ_PAIR *fq_pair);
+
+
+