2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 lrnassar Wed Jul 8 13:53:54 2026 -0700 Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched. diff --git src/hg/hgc/bigRmskClick.c src/hg/hgc/bigRmskClick.c index e7c17189b57..0f01a0ead61 100644 --- src/hg/hgc/bigRmskClick.c +++ src/hg/hgc/bigRmskClick.c @@ -1,411 +1,411 @@ /* bigRmskClick - Click handler for bigRmskTrack. This is based * loosely on the original rmsk click handler inside * of hgc.c. * * Written by Robert Hubley 10/2021 */ /* Copyright (C) 2021 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hgc.h" #include "rmskAlign.h" #include "hCommon.h" #include "chromAlias.h" struct bigRmskAlignRecord { char *chrom; /*Reference sequence chromosome or scaffold*/ unsigned chromStart; /*Start position of alignment on chromosome*/ unsigned chromEnd; /*End position of alignment on chromosome*/ unsigned chromRemain; /*Remaining bp in the chromosome or scaffold*/ float score; /*alignment score (sw, bits or evalue)*/ float percSubst; /*Base substitution percentage*/ float percDel; /*Base deletion percentage*/ float percIns; /*Bases insertion percentage*/ char strand[2]; /*Strand - either + or -*/ char *repName; /*Name of repeat*/ char *repType; /*Type of repeat*/ char *repSubtype; /*Subtype of repeat*/ unsigned repStart; /*Start in repeat sequence*/ unsigned repEnd; /*End in repeat sequence*/ unsigned repRemain; /*Remaining unaligned bp in the repeat sequence*/ unsigned id; /*The ID of the hit. Used to link related fragments*/ char *calignData; /*The alignment data stored as a single string*/ }; void printAlignmentBR (char strand, char * genoName, uint genoStart, uint genoEnd, char *repName, uint repStart, uint repEnd, char *calignData ) /* * Print RepeatMasker alignment data stored in RM's cAlign format. * The format is basically a lightly compressed diff format where * the query and subject are merged into one squence line. The * runs of exact matching sequences are interrupted by either * single base substitutions annotated as queryBase "/" subjectBase, * insertions in the subject annotated as "+ACTAT+", or deletions * in the query annotated as "-ACTTTG-". */ { int alignLength = 80; char querySeq[alignLength + 1]; char diffSeq[alignLength + 1]; char subjSeq[alignLength + 1]; int inSub = 0; int inDel = 0; int inIns = 0; int aIdx = 0; int sIdx = 0; int qCnt = 0; int sCnt = 0; uint qStart = genoStart; uint sStart = repStart; if (strand == '-') sStart = repEnd; int maxNameLen = (strlen(genoName) > strlen(repName) ? strlen(genoName) : strlen(repName)); while (calignData[aIdx] != '\0') { if (calignData[aIdx] == '/') inSub = 1; else if (calignData[aIdx] == '-') inDel ^= 1; else if (calignData[aIdx] == '+') inIns ^= 1; else { if (inSub) { subjSeq[sIdx - 1] = calignData[aIdx]; if ((querySeq[sIdx - 1] == 'C' && subjSeq[sIdx - 1] == 'T') || (querySeq[sIdx - 1] == 'T' && subjSeq[sIdx - 1] == 'C') || (querySeq[sIdx - 1] == 'A' && subjSeq[sIdx - 1] == 'G') || (querySeq[sIdx - 1] == 'G' && subjSeq[sIdx - 1] == 'A')) diffSeq[sIdx - 1] = 'i'; else if ((index ("BDHVRYKMSWNX", querySeq[sIdx - 1]) != NULL) || (index ("BDHVRYKMSWNX", subjSeq[sIdx - 1]) != NULL)) diffSeq[sIdx - 1] = '?'; else diffSeq[sIdx - 1] = 'v'; inSub = 0; } else if (inDel) { querySeq[sIdx] = calignData[aIdx]; subjSeq[sIdx] = '-'; diffSeq[sIdx] = '-'; qCnt++; sIdx++; } else if (inIns) { querySeq[sIdx] = '-'; subjSeq[sIdx] = calignData[aIdx]; diffSeq[sIdx] = '-'; sCnt++; sIdx++; } else { diffSeq[sIdx] = ' '; querySeq[sIdx] = calignData[aIdx]; subjSeq[sIdx] = calignData[aIdx]; sCnt++; qCnt++; sIdx++; } if (sIdx == alignLength) { querySeq[sIdx] = '\0'; diffSeq[sIdx] = '\0'; subjSeq[sIdx] = '\0'; printf ("%*s %10d %s %d\n", maxNameLen, genoName, qStart, querySeq, (qStart + qCnt - 1)); printf ("%*s %s\n", maxNameLen, " ", diffSeq); if (strand == '+') printf ("%*s %10d %s %d\n", maxNameLen, repName, sStart, subjSeq, (sStart + sCnt - 1)); else printf ("%*s %10d %s %d\n", maxNameLen, repName, sStart, subjSeq, (sStart - sCnt + 1)); printf ("\n"); qStart += qCnt; if (strand == '+') sStart += sCnt; else sStart -= sCnt; qCnt = 0; sCnt = 0; sIdx = 0; } } aIdx++; } if (sIdx) { querySeq[sIdx] = '\0'; diffSeq[sIdx] = '\0'; subjSeq[sIdx] = '\0'; printf ("%*s %10d %s %d\n", maxNameLen, genoName, qStart, querySeq, (qStart + qCnt - 1)); printf ("%*s %s\n", maxNameLen, " ", diffSeq); if (strand == '+') printf ("%*s %10d %s %d\n", maxNameLen, repName, sStart, subjSeq, (sStart + sCnt - 1)); else printf ("%*s %10d %s %d\n", maxNameLen, repName, sStart, subjSeq, (sStart - sCnt + 1)); } } void printOutTableHeaderBR (char strand) /* Print the appropriate HTML table header * given the strand of the element. */ { const char *hd1_style = "style=\"background-color:#C2C9E0; font-size:14px; padding:4px 14px;\""; const char *hd1span_style = "style=\"background-color:#6678B1; font-size:14px; padding:4px 14px;\""; const char *hd2_style = "style=\"background-color:#C2C9E0; font-size:14px; padding:4px 14px; " "border-bottom: 2px solid #6678B1;\""; printf (" <thead>\n"); printf (" <tr>\n"); printf (" <th %s>bit/sw</th>\n", hd1_style); printf (" <th %s>perc</th>\n", hd1_style); printf (" <th %s>perc</th>\n", hd1_style); printf (" <th %s>perc</th>\n", hd1_style); printf (" <th colspan=\"4\" %s>query</th>\n", hd1span_style); printf (" <th %s></th>\n", hd1_style); printf (" <th colspan=\"5\" %s>matching repeat</th>\n", hd1span_style); printf (" <th %s></th>\n", hd1_style); printf (" </tr>\n"); printf (" <tr>\n"); printf (" <th %s>score</th>\n", hd2_style); printf (" <th %s>div.</th>\n", hd2_style); printf (" <th %s>del.</th>\n", hd2_style); printf (" <th %s>ins.</th>\n", hd2_style); printf (" <th %s>sequence</th>\n", hd2_style); printf (" <th %s>begin</th>\n", hd2_style); printf (" <th %s>end</th>\n", hd2_style); printf (" <th %s>remaining</th>\n", hd2_style); printf (" <th %s>orient.</th>\n", hd2_style); printf (" <th %s>name</th>\n", hd2_style); printf (" <th %s>class/family</th>\n", hd2_style); if (strand == 'C') { printf (" <th %s>remaining</th>\n", hd2_style); printf (" <th %s>end</th>\n", hd2_style); printf (" <th %s>begin</th>\n", hd2_style); } else { printf (" <th %s>begin</th>\n", hd2_style); printf (" <th %s>end</th>\n", hd2_style); printf (" <th %s>remaining</th>\n", hd2_style); } printf (" <th %s>id</th>\n", hd2_style); printf (" </tr>\n"); printf (" </thead>\n"); } void doBigRmskRepeat (struct trackDb *tdb, char *item) /* Main entry point */ { cartWebStart (cart, database, "%s", tdb->longLabel); char *chrom = cartString(cart, "c"); int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); /* Open bigBed file and get interval list. */ char *fileName = trackDbSetting(tdb, "bigDataUrl"); struct bbiFile *bbi = bigBedFileOpenAlias(fileName,chromAliasFindAliases); struct lm *lm = lmInit(0); struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm); /* Find particular item in list - matching start, and item if possible. */ boolean found = FALSE; struct bigBedInterval *bb; const char *data_style = "style=\"padding:0px 6px;\""; int bedSize = bbi->fieldCount; char *fields[bedSize]; char startBuf[17], endBuf[17]; for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields, bedSize); if ( sameOk(fields[12], item) ) { found = TRUE; break; } } if ( found ) { char class[32]; class[0] = '\0'; char subclass[32]; subclass[0] = '\0'; char *poundPtr = index (fields[3], '#'); if (poundPtr) { // Terminate name string properly safecpy (class, sizeof (class), poundPtr + 1); *poundPtr = '\0'; char *slashPtr = index (class, '/'); if (slashPtr) { // Terminate class string properly safecpy (subclass, sizeof (subclass), slashPtr + 1); *slashPtr = '\0'; } } printf ("<b>Repeat:</b> %s<br>\n", fields[3]); printf ("<b>Class:</b> %s<br>\n", class); printf ("<b>Subclass:</b> %s<br>\n", subclass); printf ("<b>Orientation:</b> %s<br>\n", fields[5]); //printf ("<b>Joined Element Genomic Range:</b> %s:%d-%d<br>\n", //rmJoin->chrom, rmJoin->alignStart+1, rmJoin->alignEnd); printf ("<br><br>\n"); printf ("<h4>RepeatMasker Joined Annotations:</h4>\n"); printf ("The RepeatMasker annotation line(s) for this element. " "If the element is fragmented the output will contain one " "line per joined fragment.<p>\n"); printf ("<table cellspacing=\"0\">\n"); char *description = fields[13]; printOutTableHeaderBR(*fields[5]); char *outLine; char *outLineTok = description; while ((outLine = strsep(&outLineTok,",")) != NULL) { char *outField; char *outFieldTok = outLine; printf (" <tr>\n"); while ((outField = strsep(&outFieldTok," ")) != NULL) { printf (" <td %s>%s</td>\n", data_style, outField); } printf (" <td>\n"); printf ("<A HREF=\"%s&db=%s&position=%s%%3A%d-%s\">Browser</A>", hgTracksPathAndSettings (), database, fields[0], atoi(fields[6]) + 1, fields[7]); char *tbl = cgiUsualString ("table", cgiString ("g")); - printf (" - <A HREF=\"%s&o=%s&g=getDna&i=%s&c=%s&l=%s&r=%s&" + printf (" - <A HREF=\"%s&db=%s&o=%s&g=getDna&i=%s&c=%s&l=%s&r=%s&" "strand=%s&table=%s\">" - "DNA</A>\n", hgcPathAndSettings (), fields[6], + "DNA</A>\n", hgcPathAndSettings (), database, fields[6], (fields[3] != NULL ? cgiEncode (fields[3]) : ""), fields[0], fields[6], fields[7], cgiEncode (fields[5]), tbl); printf (" </td>\n"); printf (" </tr>\n"); } printf("</table>\n"); } else { printf("No item %s starting at %d\n", emptyForNull(item), start); } lmCleanup(&lm); bbiFileClose(&bbi); /* * Locate *.align data for this element */ char *xrefDataUrl = trackDbSetting(tdb, "xrefDataUrl"); if ( xrefDataUrl ) { //struct bbiFile *abbi = bigBedFileOpen(xrefDataUrl); struct bbiFile *abbi = bigBedFileOpenAlias(xrefDataUrl,chromAliasFindAliases); struct lm *alm = lmInit(0); struct bigBedInterval *abbList = bigBedIntervalQuery(abbi, chrom, start, end, 0, alm); printf ("<h4>RepeatMasker Alignments:</h4>\n"); printf ("The raw alignment data used by RepeatMasker to generate " "the final annotation call for this element. NOTE: The " "aligned sequence names and consensus positions may differ " "from the final annotation.<p>\n"); printf ("<table>\n"); struct bigRmskAlignRecord *arec = NULL; AllocVar(arec); for (bb = abbList; bb != NULL; bb = bb->next) { char *afields[abbi->fieldCount]; bigBedIntervalToRow(bb, chrom, startBuf, endBuf, afields, abbi->fieldCount); if ( sameOk(afields[15], item) ) { arec->chrom = afields[0]; arec->chromStart = sqlUnsigned(afields[1]); arec->chromEnd = sqlUnsigned(afields[2]); arec->chromRemain = sqlUnsigned(afields[3]); arec->score = sqlFloat(afields[4]); arec->percSubst = sqlFloat(afields[5]); arec->percDel = sqlFloat(afields[6]); arec->percIns = sqlFloat(afields[7]); safef(arec->strand, sizeof(arec->strand), "%s", afields[8]); arec->repName = afields[9]; arec->repType = afields[10]; arec->repSubtype = afields[11]; arec->repStart = sqlUnsigned(afields[12]); arec->repEnd = sqlUnsigned(afields[13]); arec->repRemain = sqlUnsigned(afields[14]); arec->id = sqlUnsigned(afields[15]); arec->calignData = afields[16]; printf (" <tr>\n"); printf (" <td>%.2f</td>\n", arec->score); printf (" <td>%3.2f</td>\n", arec->percSubst); printf (" <td>%3.2f</td>\n", arec->percDel); printf (" <td>%3.2f</td>\n", arec->percIns); printf (" <td>%s</td>\n", arec->chrom); printf (" <td>%d</td>\n", arec->chromStart + 1); printf (" <td>%d</td>\n", arec->chromEnd); printf (" <td>(%d)</td>\n", arec->chromRemain); printf (" <td>%s</td>\n", arec->strand); printf (" <td>%s</td>\n", arec->repName); printf (" <td>%s/%s</td>\n", arec->repType, arec->repSubtype); if (arec->strand[0] == '-') { printf (" <td>(%d)</td>\n", arec->repRemain); printf (" <td>%d</td>\n", arec->repEnd); printf (" <td>%d</td>\n", arec->repStart); } else { printf (" <td>%d</td>\n", arec->repStart); printf (" <td>%d</td>\n", arec->repEnd); printf (" <td>(%d)</td>\n", arec->repRemain); } printf (" <td>%d</td>\n", arec->id); printf (" </tr><tr><td colspan=\"15\"><pre>\n"); printAlignmentBR ( arec->strand[0], arec->chrom, arec->chromStart, arec->chromEnd, arec->repName, arec->repStart, arec->repEnd, arec->calignData ); printf (" </pre><td></tr>\n"); } } //for(bb = abblist.... printf ("</table>\n"); lmCleanup(&alm); bbiFileClose(&abbi); } // if ( xref... printTrackHtml(tdb); }