static boolean isAdjacentFrames(struct exonFrames *ef0, struct exonFrames *ef1)
/* check if exonFrames objects are adjacent and should be joined. ef0 preceeds
* ef1 in the direction of transcription. Must be i */
{
if (ef0->mf.strand[0] == '+')
return (ef1->mf.chromStart == ef0->mf.chromEnd)
&& (ef1->mf.frame == frameIncr(ef0->mf.frame, (ef0->mf.chromEnd-ef0->mf.chromStart)));
else
return (ef1->mf.chromEnd == ef0->mf.chromStart)
&& (ef1->mf.frame == frameIncr(ef0->mf.frame, (ef0->mf.chromEnd-ef0->mf.chromStart)));
}
static boolean isSplitCodon(struct exonFrames *ef0, struct exonFrames *ef1)
/* Determine if the last codon of ef0 is split across maf blocks and is
* continued in ef1. If codon is not split, or only partially aligned, false
* is returned. ef0 preceeds ef1 in the direction of transcription */
{
int tLen0 = ef0->mf.chromEnd - ef0->mf.chromStart;
if (ef1->cdsStart != ef0->cdsEnd)
return FALSE; /* deletion in gene between two records */
if (frameIncr(ef0->mf.frame, tLen0) == 0)
return FALSE; /* codon not split */
if (ef1->mf.frame != frameIncr(ef0->mf.frame, tLen0))
return FALSE; /* frame not contiguous */
return TRUE;
}
static struct codonCoords findLastCodon(struct genePred *gp, int *frames)
/* get the coordinates of the last codon (start or stop). It must be in
* correct frame, or zero is returned. */
{
if (honorCdsStat && (gp->optFields & genePredCdsStatFld)
&& (gp->cdsEndStat != cdsComplete))
return zeroCodonCoords; // not flagged as complete
// find last CDS exon
int iExon, cdsStart = 0, cdsEnd = 0;
for (iExon = gp->exonCount-1; iExon >= 0; iExon--)
{
if (genePredCdsExon(gp, iExon, &cdsStart, &cdsEnd))
break;
}
if (iExon == -1)
return zeroCodonCoords; // no CDS
// get frame of last base and validate that we are on a bound.
int frame = (gp->strand[0] == '-') ? frames[iExon]
: frameIncr(frames[iExon], (cdsEnd-cdsStart));
if (frame != 0)
return zeroCodonCoords; // not on a frame boundary
/* get last part of codon */
struct codonCoords codon = zeroCodonCoords;
codon.start= codon.start1 = max(cdsStart, cdsEnd-3);
codon.end = codon.end1 = cdsEnd;
codon.iExon1 = iExon;
/* first part, if spliced */
if ((codon.end1 - codon.start1) < 3)
{
codon.start2 = codon.start1;
codon.end = codon.end2 = codon.end1;
codon.iExon2 = iExon;
iExon--;
codon.iExon1 = iExon;
if ((iExon == -1) || !genePredCdsExon(gp, iExon, &cdsStart, &cdsEnd))
return zeroCodonCoords; // no more
int needed = 3 - (codon.end2 - codon.start2);
if ((cdsEnd - cdsStart) < needed)
return zeroCodonCoords; // not enough space
codon.start = codon.start1 = cdsEnd-needed;
codon.end1 = cdsEnd;
}
return codon;
}
