/* Stuff shared across modules. */

/* Copyright (C) 2008 The Regents of the University of California 
 * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */

struct linkedBeds
/* A list of beds that are from the same transcript with
 * possible soft edges between them. */
    {
    struct linkedBeds *next;
    struct bed *bedList;	/* Nonempty list of beds, order is important */
    char *sourceType;		/* "mrna", "refSeq", etc. not alloced here */
    int chromStart,chromEnd;	/* Bounds in genome. */
    int id;			/* Corresponds to source ID when filled in. */
    };

struct txGraph *makeGraph(struct linkedBeds *lbList, int maxBleedOver, 
	int maxUncheckedBleed, struct nibTwoCache *seqCache,
	double singleExonMaxOverlap, char *name);
/* Create a graph corresponding to linkedBedsList.
 * The maxBleedOver parameter controls how much of a soft edge that
 * can be cut off when snapping to a hard edge.  The singleExonMaxOverlap
 * controls what ratio of a single exon transcript can overlap spliced 
 * transcripts */

boolean trustedSource(char *sourceType);
/* Return TRUE source type is trusted (refSeq or something similar). */ 

boolean noCutSource(char *sourceType);
/* Return TRUE if source is not to be truncated during snap to operation. */