combine_reads.h

#ifndef _FLASH_COMBINE_READS_H_
#define _FLASH_COMBINE_READS_H_

#include <stdbool.h>

struct read;

/* Parameters for the core algorithm of FLASH.  See the help output for more
 * information.  */
struct combine_params {
	/* --min-overlap  */
	int min_overlap;
    

	/* --min-overlap-outie */
	int min_overlap_outie;

	/* --max-overlap  */
	int max_overlap;

	/* --max-mismatch-density  */
	float max_mismatch_density;

	/* --cap-mismatch-quals  */
	bool cap_mismatch_quals;

	/* --allow-outies  */
	bool allow_outies;

    /* --skip-overlap (just does adapter trimming*/
    bool skip_overlap;

	bool discard_reads;
	int percent_cutoff;
	int qual_score_cutoff;
	
};

/* Result of a call to combine_reads()  */
enum combine_status {
	/* The reads could not be combined.  */
	NOT_COMBINED = 0,

	JUNK_READ = -5,
	/* The reads were combined in "innie" orientation, like the following:
	 *
	 * ---------->
	 *     <------------
	 *
	 * (Note: read_2 is reverse complemented before the call to
	 * combine_reads()).  */
	COMBINED_AS_INNIE,

	/* The reads were combined in "outie" orientation, like the following:
	 *
	 * <----------
	 *     ------------>
	 *
	 * (Note: read_2 is reverse complemented before the call to
	 * combine_reads()).  */
	COMBINED_AS_OUTIE,
};

extern enum combine_status
combine_reads(const struct read *read_1, const struct read *read_2,
	      struct read *combined_read,
	      const struct combine_params *params);

#endif /* _FLASH_COMBINE_READS_H_  */