/* Splat.h - link together exported things from various splat modules. */

extern char *version ;	/* Program version number. */

struct splatHit
/* Information on an index hit.  This only has about a 1% chance of being real after
 * extension, but hey, it's a start. */
    {
    struct splatHit *next;	/* Next in list. */
    bits32 tOffset;	/* Offset to DNA in target */
    int gapSize;	/* >0 for insert in query/del in target, <0 for reverse. 0 for no gap. */
    int subCount;	/* Count of substitutions we know about already. */
    int missingQuad;	/* Which data quadrant is lacking (not found in index). */
    };

struct splatTag
/* Roughtly 25-base match that passes maxGap and maxMismatch criteria. */
    {
    struct splatTag *next;	 /* Next in list. */
    int divergence;  /* mismatch + 2*inserts for now. */
    bits32 q1,t1;  /* Position of first block in query and target. */
    bits32 size1;	/* Size of first block. */
    bits32 q2,t2;  /* Position of second block if any. */
    bits32 size2;  /* Size of second block.  May be zero. */
    char strand; /* Query strand. */
    };
#define splatTagFree(pt) freez(pt)
#define splatTagFreeList(pList) slFreeList(pList)

struct splatAlign
/* A full alignment - the first 25 bases plus if need be a banded extension. */
    {
    struct splatAlign *next;	/* Next in list. */
    struct chain *chain;	/* Chain representation. */
    DNA *qDna;			/* Query sequence DNA.  Not allocated here. */
    DNA *tDna;			/* Target sequence DNA.  Not allocated here. */
    };

void splatAlignFree(struct splatAlign **pAli);
/* Free up a splatAlign. */

void splatAlignFreeList(struct splatAlign **pList);
/* Free up a list of splatAligns. */

struct splatAlign *splatExtendTags(struct splatTag *tagList, 
	struct dnaSeq *qSeqF, struct dnaSeq *qSeqR, struct splix *splix,
	struct axtScoreScheme *scoreScheme);
/* Convert a list of tags to a list of alignments. */

int countDnaDiffs(DNA *a, DNA *b, int size);
/* Count number of differing bases. */

void splatOutHeader(char *target, char *query, char *outType, FILE *f);
/* Output file header if any.  Also check and abort if outType is not supported. */

void splatOutList(struct splatAlign *aliList, char *outType,
	struct dnaSeq *qSeqF, struct dnaSeq *qSeqR, struct splix *splix, FILE *f);
/* Output list of alignments to file in format defined by outType. */

void overRead(char *fileName, int minCount, int *retArraySize, bits64 **retArray);
/* Read in file of format <25-mer> <count> and return an array the 25-mers that have
 * counts greater or equal to minCount.  The 25-mers will be returned as 64-bit numbers
 * with the DNA packed 2 bits per base. */

boolean overCheck(bits64 query, int arraySize, bits64 *array);
/* Return TRUE if query is in array.  */