/* lrg.h was originally generated by the autoSql program, which also 
 * generated lrg.c and lrg.sql.  This header links the database and
 * the RAM representation of objects. */

/* Copyright (C) 2013 The Regents of the University of California 
 * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

#ifndef LRG_H
#define LRG_H

#define LRG_NUM_COLS 21

extern char *lrgCommaSepFieldNames;

struct lrg
/* Locus Reference Genomic regions */
    {
    struct lrg *next;  /* Next in singly linked list. */
    char *chrom;	/* Reference assembly chromosome or scaffold */
    unsigned chromStart;	/* Start position in chromosome */
    unsigned chromEnd;	/* End position in chromosome */
    char *name;	/* LRG ID */
    unsigned score;	/* Placeholder for BED format compatibility (0) */
    char strand[2];	/* Orientation of LRG to reference assembly: + or - */
    unsigned thickStart;	/* Placeholder for BED format compatibility (same as chromStart) */
    unsigned thickEnd;	/* Placeholder for BED format compatibility (same as chromEnd) */
    unsigned reserved;	/* Placeholder for BED format compatibility (0) */
    int blockCount;	/* Number of gapless aligned blocks */
    int *blockSizes;	/* Comma separated list of block sizes */
    int *chromStarts;	/* Start positions relative to chromStart */
    char *mismatches;	/* List of bases that differ between LRG and reference assembly */
    char *indels;	/* List of insertions/deletions in LRG and reference assembly */
    unsigned lrgSize;	/* Length in bases of LRG sequence */
    int hgncId;	/* Numeric HGNC gene identifier */
    char *hgncSymbol;	/* HGNC gene symbol */
    char *ncbiAcc;	/* NCBI accession of LRG sequence */
    char *lrgSource;	/* Source of LRG sequence */
    char *lrgSourceUrl;	/* URL of lrgSource */
    char *creationDate;	/* Date on which this sequence was added as a LRG */
    };

struct lrg *lrgLoad(char **row);
/* Load a lrg from row fetched with select * from lrg
 * from database.  Dispose of this with lrgFree(). */

struct lrg *lrgLoadAll(char *fileName);
/* Load all lrg from whitespace-separated file.
 * Dispose of this with lrgFreeList(). */

struct lrg *lrgLoadAllByChar(char *fileName, char chopper);
/* Load all lrg from chopper separated file.
 * Dispose of this with lrgFreeList(). */

#define lrgLoadAllByTab(a) lrgLoadAllByChar(a, '\t');
/* Load all lrg from tab separated file.
 * Dispose of this with lrgFreeList(). */

struct lrg *lrgCommaIn(char **pS, struct lrg *ret);
/* Create a lrg out of a comma separated string. 
 * This will fill in ret if non-null, otherwise will
 * return a new lrg */

void lrgFree(struct lrg **pEl);
/* Free a single dynamically allocated lrg such as created
 * with lrgLoad(). */

void lrgFreeList(struct lrg **pList);
/* Free a list of dynamically allocated lrg's */

void lrgOutput(struct lrg *el, FILE *f, char sep, char lastSep);
/* Print out lrg.  Separate fields with sep. Follow last field with lastSep. */

#define lrgTabOut(el,f) lrgOutput(el,f,'\t','\n');
/* Print out lrg as a line in a tab-separated file. */

#define lrgCommaOut(el,f) lrgOutput(el,f,',',',');
/* Print out lrg as a comma separated list including final comma. */

/* -------------------------------- End autoSql Generated Code -------------------------------- */


struct psl *lrgToPsl(struct lrg *lrg, uint chromSize);
/* Use lrg's mismatches and indels to make a PSL. */

struct dnaSeq *lrgReconstructSequence(struct lrg *lrg, char *db);
/* Use genomic sequence, lrg->mismatches and lrg->indels to reconstruct LRG sequence */

struct lrgDiff
/* Locus Reference Genomic <mapping><diff> item condensed into coordinates and sequences:
 * an alignment gap block.  When lrg->strand is "-", chromSeq is reverse-complemented
 * but chromosome coordinates are still on + strand. */
{
    struct lrgDiff *next;
    uint chromStart;
    uint chromEnd;
    char *chromSeq;
    uint lrgStart;
    uint lrgEnd;
    char *lrgSeq;
};

struct lrgDiff *lrgParseMismatches(struct lrg *lrg);
/* Parse lrg->mismatches and return a list of lrgDiffs. */

struct lrgDiff *lrgParseIndels(struct lrg *lrg);
/* Parse lrg->indels and return a list of lrgDiffs. */

void lrgDiffFreeList(struct lrgDiff **pDiff);
/* Free up a list of parsed diffs. */

#endif /* LRG_H */