e4b95e1845f752954f388a0c61b7d4a107baa80a
braney
  Wed May 27 18:02:07 2020 -0700
don't count frameshifts as small introns

diff --git src/hg/lib/variantProjector.c src/hg/lib/variantProjector.c
index 760c347..24b367f 100644
--- src/hg/lib/variantProjector.c
+++ src/hg/lib/variantProjector.c
@@ -75,31 +75,31 @@
 }
 
 // Google search on "minimal intron size" turned up a study of shortest known introns, ~48-50 in
 // most species surveyed at the time.
 #define MIN_INTRON 45
 
 static boolean pslIntronTooShort(struct psl *psl, int blkIx, int minIntronSize)
 /* Return TRUE if the target gap between blkIx and blkIx+1 is too short to be a plausible intron. */
 {
 if (blkIx >= psl->blockCount - 1 || blkIx < 0)
     errAbort("pslIntronTooShort: %s blkIx %d is out of range [0, %d]",
              psl->qName, blkIx, psl->blockCount - 1);
 int tGapLen = psl->tStarts[blkIx+1] - psl->tStarts[blkIx] - psl->blockSizes[blkIx];
 int qGapLen = psl->qStarts[blkIx+1] - psl->qStarts[blkIx] - psl->blockSizes[blkIx];
 int intronLen = tGapLen - qGapLen;
-return (intronLen < minIntronSize);
+return (intronLen > 0) && (intronLen < minIntronSize);
 }
 
 void vpPosGenoToTx(uint gOffset, struct psl *txAli, struct vpTxPosition *txPos, boolean isTxEnd)
 /* Use txAli to project gOffset onto transcript-relative coords in txPos.
  * Set isTxEnd to TRUE if we are projecting to the end coordinate in transcript space:
  * higher genomic coord if transcript on '+' strand, lower genomic coord if tx on '-' strand. */
 {
 ZeroVar(txPos);
 txPos->gOffset = gOffset;
 boolean isRc = (pslQStrand(txAli) == '-');
 // Coordinate transforms of start and end coordinates can be done the same way, but
 // when determining which region of the transcript the variant falls in, we need to
 // treat the open end differently (looking backward) from the closed start (looking forward).
 int endCmp = (isTxEnd != isRc) ? 1 : 0;
 int gOffsetCmp = gOffset - endCmp;