void sqlSignedDynamicArray(char *s, int **retArray, int *retSize)
/* Convert comma separated list of numbers to an dynamically allocated
* array, which should be freeMem()'d when done. */
{
int *sArray, *dArray = NULL;
int size;
sqlSignedStaticArray(s, &sArray, &size);
if (size > 0)
{
AllocArray(dArray,size);
CopyArray(sArray, dArray, size);
}
*retArray = dArray;
*retSize = size;
}
static char *computeFrames(struct bed *bed, char *exonFrames, int *retStartIndx, int *retStopIndx)
/* Compute frames, in order dictated by strand. bed must be BED12.
* Convert exonFrames to gtf frame if available. */
{
int *ef;
if (exonFrames)
{
int efSize = 0;
sqlSignedStaticArray(exonFrames, &ef, &efSize); // not thread safe.
if (efSize != bed->blockCount)
errAbort("Unexpected error, name=%s blockCount=%d but exonFrames size = %d", bed->name, bed->blockCount, efSize);
}
char *frames = needMem(bed->blockCount);
boolean gotFirstCds = FALSE;
int nextPhase = 0, startIndx = 0, stopIndx = 0;
// If lack of thick region has been represented this way, fix:
if (bed->thickStart == 0 && bed->thickEnd == 0)
bed->thickStart = bed->thickEnd = bed->chromStart;
int i;
for (i=0; i < bed->blockCount; i++)
{
int j = (bed->strand[0] == '-') ? bed->blockCount-i-1 : i;
int exonStart = bed->chromStart + bed->chromStarts[j];
int exonEnd = exonStart + bed->blockSizes[j];
if ((exonStart < bed->thickEnd) && (exonEnd > bed->thickStart))
{
int cdsS = max(exonStart, bed->thickStart);
int cdsE = min(exonEnd, bed->thickEnd);
int cdsSize = cdsE - cdsS;
if (! gotFirstCds)
{
gotFirstCds = TRUE;
startIndx = j;
}
if (exonFrames)
{
int n = ef[j];
char c = '.'; // -1 exonFrame becomes '.' in gtf
if (n == 0)
c = '0';
else if (n == 1) // gtf frames are really "phases", so 1 and 2 swap.
c = '2';
else if (n == 2)
c = '1';
frames[j] = c;
}
else
{
frames[j] = '0' + nextPhase;
nextPhase = (3 + ((nextPhase - cdsSize) % 3)) % 3;
}
stopIndx = j;
}
else
{
frames[j] = '.';
}
}
if (retStartIndx)
*retStartIndx = startIndx;
if (retStopIndx)
*retStopIndx = stopIndx;
return frames;
}
