e323d595c241d03570d380d8c60de60e99c1c4ec braney Fri Mar 21 12:36:21 2025 -0700 add support for bigDbSnp to quicklift diff --git src/hg/hgTracks/bigBedTrack.c src/hg/hgTracks/bigBedTrack.c index c28a2322e19..83573fd0ac0 100644 --- src/hg/hgTracks/bigBedTrack.c +++ src/hg/hgTracks/bigBedTrack.c @@ -691,31 +691,31 @@ lf = lfFromPslx(psl, sizeMul, isXeno, nameGetsPos, track); lf->original = psl; if ((seq != NULL) && (lf->orientation == -1)) reverseComplement(seq, strlen(seq)); lf->extra = seq; lf->cds = cds; lf->useItemRgb = useItemRgb; if ( lf->useItemRgb ) lf->filterColor = itemRgbColumn(bedRow[8]); } else if (sameString(tdb->type, "bigDbSnp")) { // bigDbSnp does not have a score field, but I want to compute the freqSourceIx from // trackDb and settings one time instead of for each item, so I'm overloading scoreMin. int freqSourceIx = scoreMin; - lf = lfFromBigDbSnp(tdb, bb, filters, freqSourceIx, bbi); + lf = lfFromBigDbSnp(tdb, bb, filters, freqSourceIx, bbi, chainHash); } else { char startBuf[16], endBuf[16]; bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow)); if (bigBedFilterInterval(bbi, bedRow, filters)) { if (quickLiftFile) { if ((bed = quickLiftIntervalsToBed(bbi, chainHash, bb)) != NULL) { bedCopy = cloneBed(bed); lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount, scoreMin, scoreMax, useItemRgb); }