b91a917e39c8d58d0de5e6325606f098ef0fb60b
angie
  Wed Mar 21 09:22:21 2018 -0700
New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts.
Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed.
This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track.  refs #21079

diff --git src/hg/lib/hgHgvs.c src/hg/lib/hgHgvs.c
index c26718f..340f406 100644
--- src/hg/lib/hgHgvs.c
+++ src/hg/lib/hgHgvs.c
@@ -2893,31 +2893,31 @@
 if (dupLen == 0 && isIns)
     {
     // Expand insertion point to 2-base region around insertion point for HGVS.
     // startPos = base to left of endPos whose region looks left/5';
     // endPos = base to right of startPos whose region looks right/3'.
     struct vpTxPosition newStart = *endPos;
     vpTxPosSlideInSameRegion(&newStart, -1);
     struct vpTxPosition newEnd = *startPos;
     vpTxPosSlideInSameRegion(&newEnd, 1);
     *startPos = newStart;
     *endPos = newEnd;
     }
 return dupLen;
 }
 
-static uint hgvsTxToCds(uint txOffset, struct genbankCds *cds, boolean isStart, char pPrefix[2])
+uint hgvsTxToCds(uint txOffset, struct genbankCds *cds, boolean isStart, char pPrefix[2])
 /* Return the cds-relative HGVS coord and prefix corresponding to 0-based txOffset & cds. */
 {
 // Open end adjustment for determining CDS/UTR region:
 int endCmp = isStart ? 0 : 1;
 // For adjusting non-negative coords to HGVS's positive 1-based closed:
 int oneBased = isStart ? 1 : 0;
 // For adjusting negative coords to HGVS's negative 0-based closed:
 int closedEnd = isStart ? 0 : 1;
 pPrefix[1] = '\0';
 uint cdsCoord = 0;
 if (txOffset - endCmp < cds->start)
     {
     // 5'UTR: coord is negative distance from cdsStart
     pPrefix[0] = '-';
     cdsCoord = cds->start - txOffset + closedEnd;