04f1eb41233f2cd7dd80fb51f36eda1462f2899f angie Wed Mar 3 15:26:23 2021 -0800 Code review feedback: ';;' --> ';'. refs #27102 diff --git src/hg/lib/variantProjector.c src/hg/lib/variantProjector.c index ca94850..f0a926e 100644 --- src/hg/lib/variantProjector.c +++ src/hg/lib/variantProjector.c @@ -330,31 +330,31 @@ reverseComplement(buf, splicedLen); } static boolean genomeTxMismatch(char *txRef, struct seqWindow *gSeqWin, uint gStart, uint gEnd, struct psl *txAli) /* If the variant overlaps aligned blocks then compare spliced strand-corrected genomic reference * sequence with transcript reference sequence. vpTx start, end and txRef must be in place. * Note: this will detect substitutions but not indels by design -- leave it to processIndels * and vpTxSetTxAlt to detect indel mismatches. */ { boolean mismatch = FALSE; if (isNotEmpty(txRef)) { // Watch out for overlapping blocks due to ribosomal slippage as in SARS-CoV-2. int fudge = 3; - int bufLen = gEnd - gStart + 1 + fudge;; + int bufLen = gEnd - gStart + 1 + fudge; char splicedGSeq[bufLen]; splicedGSeq[0] = '\0'; spliceGenomicInRange(gSeqWin, gStart, gEnd, txAli, FALSE, splicedGSeq, sizeof(splicedGSeq)); if (isNotEmpty(splicedGSeq) && differentString(splicedGSeq, txRef)) mismatch = TRUE; } return mismatch; } boolean vpTxPosIsInsertion(struct vpTxPosition *startPos, struct vpTxPosition *endPos) /* Return TRUE if startPos and endPos describe a zero-length region. */ { // Sometimes an insertion happens at the boundary between regions, in which case startPos->region // and endPos->region will be different even though they land on the same point. // At the boundary, endPos->region is looking left/5' and startPos->region is looking right/3'.