80daf93864f5609f6b7695766a78edd90cac0c1d braney Fri Jul 31 12:29:05 2026 -0700 quickLift: accept broadPeak tracks, and make lifted peak details right. refs #37970 Add broadPeak to the types validateOneTdb will lift; hgTracks already knew how to load one. Make hgc's encodePeak handler read the table out of the source assembly and lift the items, instead of looking in the destination assembly where the table does not exist and coming up empty. Lift peaks with a new quickLiftPeaks() rather than casting them to bed and calling quickLiftBeds(), whose thickStart and thickEnd assignments land on signalValue and pValue in struct encodePeak. diff --git src/hg/hgc/encodeClick.c src/hg/hgc/encodeClick.c index 3ec564cc1f6..02b9f15002b 100644 --- src/hg/hgc/encodeClick.c +++ src/hg/hgc/encodeClick.c @@ -1,330 +1,408 @@ /* Handle details page for ENCODE tracks. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "cart.h" #include "hgc.h" #include "hCommon.h" #include "hgColors.h" #include "customTrack.h" #include "web.h" #include "encode/encodePeak.h" #include "peptideMapping.h" #include "chromAlias.h" +#include "quickLift.h" +#include "trackHub.h" #ifdef UNUSED static boolean pairInList(struct slPair *pair, struct slPair *list) /* Return TRUE if pair is in list. */ { struct slPair *el; for (el = list; el != NULL; el = el->next) if (sameString(pair->name, el->name) && sameString(pair->val, el->val)) return TRUE; return FALSE; } static boolean selGroupListMatch(struct trackDb *tdb, struct slPair *selGroupList) /* Return TRUE if tdb has match to every item in selGroupList */ { char *subGroups = trackDbSetting(tdb, "subGroups"); if (subGroups == NULL) return FALSE; struct slPair *groupList = slPairFromString(subGroups); struct slPair *selGroup; for (selGroup = selGroupList; selGroup != NULL; selGroup = selGroup->next) { if (!pairInList(selGroup, groupList)) return FALSE; } return TRUE; } static void rAddMatching(struct trackDb *tdb, struct slPair *selGroupList, struct slName **pList) /* Add track and any descendents that match selGroupList to pList */ { if (selGroupListMatch(tdb, selGroupList)) slNameAddHead(pList, tdb->track); struct trackDb *sub; for (sub = tdb->subtracks; sub != NULL; sub = sub->next) rAddMatching(sub, selGroupList, pList); } #endif//def UNUSED static void printPeak(char **row, int rowOffset, char *item, char *chrom, int start, int end, enum encodePeakType peakType) { char **rowPastOffset = row + rowOffset; if ((sqlUnsigned(rowPastOffset[1]) != start) || (sqlUnsigned(rowPastOffset[2]) != end)) return; if (!sameString(rowPastOffset[3], item)) return; float signal = -1; float pValue = -1; float qValue = -1; /* Name */ if (rowPastOffset[3][0] != '.') printf("<B>Name:</B> %s<BR>\n", rowPastOffset[3]); /* Position */ printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n", hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end); /* Print peak base */ if ((peakType == narrowPeak) || (peakType == encodePeak)) { int peak = sqlSigned(rowPastOffset[9]); if (peak > -1) printf("<B>Peak point:</B> %d<BR>\n", start + peak + 1); // one based } /* Strand, score */ if (rowPastOffset[5][0] != '.') printf("<B>Strand:</B> %c<BR>\n", rowPastOffset[5][0]); printf("<B>Score:</B> %d<BR>\n", sqlUnsigned(rowPastOffset[4])); /* signalVal, pVal */ if (peakType != gappedPeak) { signal = sqlFloat(rowPastOffset[6]); pValue = sqlFloat(rowPastOffset[7]); qValue = sqlFloat(rowPastOffset[8]); } else { signal = sqlFloat(rowPastOffset[12]); pValue = sqlFloat(rowPastOffset[13]); qValue = sqlFloat(rowPastOffset[14]); } if (signal >= 0) printf("<B>Signal value:</B> %.3f<BR>\n", signal); if (pValue >= 0) printf("<B>P-value (-log10):</B> %.3f<BR>\n", pValue); if (qValue >= 0) printf("<B>Q-value (FDR): </B> %.3f<BR>\n", qValue); } +static void printLiftedPeak(struct encodePeak *peak, char *item, char *chrom, int start, int end, + enum encodePeakType peakType) +/* Print a quickLifted peak. Like printPeak, but works from the loaded structure since + * the item has been mapped out of the source assembly and there is no SQL row to print. */ +{ +if ((peak->chromStart != start) || (peak->chromEnd != end)) + return; +if (!sameString(peak->name, item)) + return; + +if (peak->name[0] != '.') + printf("<B>Name:</B> %s<BR>\n", peak->name); +printf("<B>Position:</B> " + "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n", + hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end); +if (((peakType == narrowPeak) || (peakType == encodePeak)) && (peak->peak > -1)) + printf("<B>Peak point:</B> %d<BR>\n", start + peak->peak + 1); // one based +if (peak->strand[0] != '.') + printf("<B>Strand:</B> %c<BR>\n", peak->strand[0]); +printf("<B>Score:</B> %d<BR>\n", peak->score); +if (peak->signalValue >= 0) + printf("<B>Signal value:</B> %.3f<BR>\n", peak->signalValue); +if (peak->pValue >= 0) + printf("<B>P-value (-log10):</B> %.3f<BR>\n", peak->pValue); +if (peak->qValue >= 0) + printf("<B>Q-value (FDR): </B> %.3f<BR>\n", peak->qValue); +} + +static ItemLoader2 peakLoaderForType(enum encodePeakType peakType) +/* Return the loader that reads a SQL row of the given peak type. */ +{ +switch(peakType) + { + case narrowPeak: + return (ItemLoader2)narrowPeakLoad; + case broadPeak: + return (ItemLoader2)broadPeakLoad; + case gappedPeak: + return (ItemLoader2)gappedPeakLoad; + case encodePeak: + return (ItemLoader2)encodePeakLoad; + default: + errAbort("bad value for peak type %d\n", peakType); + } +return NULL; +} + void doBigEncodePeak(struct trackDb *tdb, struct customTrack *ct, char *item) /* details for encodePeak type tracks. */ { enum encodePeakType peakType = narrowPeak; char *chrom = cartString(cart,"c"); int start = cgiInt("o"); int end = cgiInt("t"); boolean firstTime = TRUE; //peakType = encodePeakInferTypeFromTable(db, table, tdb->type); if (peakType == 0) errAbort("unrecognized peak type from table %s", tdb->table); genericHeader(tdb, NULL); // genericClickHandlerPlus gets there first anyway (maybe except for encodePeak custom tracks). char *fileName = bbiNameFromSettingOrTable(tdb, NULL, tdb->table); struct bbiFile *bbi = bigBedFileOpenAlias(fileName, chromAliasFindAliases); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm); int fieldCount = 10; char *bedRow[fieldCount]; char startBuf[16], endBuf[16]; for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, chrom, startBuf, endBuf, bedRow, ArraySize(bedRow)); if (firstTime) firstTime = FALSE; else // print separator printf("<BR>\n"); printPeak(bedRow, 0, item, chrom, start, end, peakType); } } void doEncodePeak(struct trackDb *tdb, struct customTrack *ct, char *item) /* details for encodePeak type tracks. */ { struct sqlConnection *conn; struct sqlResult *sr; enum encodePeakType peakType; char **row; char *db; char *table = tdb->table; char *chrom = cartString(cart,"c"); int start = cgiInt("o"); int end = cgiInt("t"); int rowOffset; boolean firstTime = TRUE; /* connect to DB */ if (ct) { db = CUSTOM_TRASH; table = ct->dbTableName; } else db = database; + +// quickLifted tracks live in the source assembly, and tdb->table carries the hub_NNN_ prefix +char *liftDb = cloneString(trackDbSetting(tdb, "quickLiftDb")); +if (liftDb != NULL) + { + quickLiftResolveTable(tdb, trackHubSkipHubName(tdb->track), &table, &liftDb); + db = liftDb; + } + conn = hAllocConn(db); peakType = encodePeakInferTypeFromTable(db, table, tdb->type); if (peakType == 0) errAbort("unrecognized peak type from table %s", tdb->table); genericHeader(tdb, NULL); // genericClickHandlerPlus gets there first anyway (maybe except for encodePeak custom tracks). +if (liftDb != NULL) + { + struct hash *chainHash = newHash(12); + char *quickLiftFile = cloneString(trackDbSetting(tdb, "quickLiftUrl")); + struct encodePeak *peakList = (struct encodePeak *)quickLiftSql(conn, quickLiftFile, table, + chrom, start, end, NULL, NULL, peakLoaderForType(peakType), 0, chainHash); + struct encodePeak *liftedPeaks = quickLiftPeaks(peakList, chainHash); + + for(; liftedPeaks != NULL; liftedPeaks = liftedPeaks->next) + { + if (firstTime) + firstTime = FALSE; + else // print separator + printf("<BR>\n"); + printLiftedPeak(liftedPeaks, item, chrom, start, end, peakType); + } + } +else + { sr = hOrderedRangeQuery(conn, table, chrom, start, end, NULL, &rowOffset); while((row = sqlNextRow(sr)) != NULL) { if (firstTime) firstTime = FALSE; else // print separator printf("<BR>\n"); printPeak(row, rowOffset, item, chrom, start, end, peakType); } sqlFreeResult(&sr); + } hFreeConn(&conn); } int encodeFiveCInterCmp(const void *va, const void *vb) /* reverse sort on bed nine's reserved field which in this */ /* case is the where the strength of the interaction is stored */ { const struct bed *a = *((struct bed **)va); const struct bed *b = *((struct bed **)vb); return b->itemRgb - a->itemRgb; } void doEncodeFiveC(struct sqlConnection *conn, struct trackDb *tdb) /* Print details for 5C track */ { char *interTable = trackDbRequiredSetting(tdb, "interTable"); char *interTableKind = trackDbRequiredSetting(tdb, "interTableKind"); char **row; char *chrom = cartString(cart,"c"); int start = cgiInt("o"); int end = cgiInt("t"); int rowOffset; int outCount = 0; struct sqlResult *sr; struct bed *interList = NULL, *inter; genericHeader(tdb, NULL); sr = hOrderedRangeQuery(conn, interTable, chrom, start, end, NULL, &rowOffset); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n", hgTracksPathAndSettings(), database, chrom, start+1, end, chrom, start+1, end); while ((row = sqlNextRow(sr)) != NULL) { inter = bedLoadN(row + rowOffset, 9); slAddHead(&interList, inter); } slSort(&interList, encodeFiveCInterCmp); webNewSection("Top %s interations", interTableKind); webPrintLinkTableStart(); webPrintLabelCell("Position"); webPrintLabelCell("5C signal"); webPrintLabelCell("Distance"); webPrintLinkTableNewRow(); for (inter = interList; inter != NULL; inter = inter->next) { char s[1024]; int distance = 0; safef(s, sizeof(s), "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>", hgTracksPathAndSettings(), database, chrom, inter->thickStart+1, inter->thickEnd, chrom, inter->thickStart+1, inter->thickEnd); webPrintLinkCell(s); safef(s, sizeof(s), "%d", inter->itemRgb); webPrintLinkCell(s); if (start > inter->thickStart) distance = inter->thickEnd - start; else distance = inter->thickStart - end; safef(s, sizeof(s), "%d", distance); webPrintLinkCell(s); if (++outCount == 50) break; if (inter->next != NULL) webPrintLinkTableNewRow(); } webPrintLinkTableEnd(); sqlFreeResult(&sr); } void doPeptideMapping(struct sqlConnection *conn, struct trackDb *tdb, char *item) /* Print details for a peptideMapping track. */ { char *chrom = cartString(cart,"c"); int start = cgiInt("o"); int end = cgiInt("t"); char query[256]; char **row; struct sqlResult *sr; struct peptideMapping pos; int rowOffset = 0; // skip bin field int found = 0; genericHeader(tdb, NULL); /* Just get the current item. */ sqlSafef(query, sizeof(query), "select * from %s where name='%s' and chrom='%s' and chromStart=%d and chromEnd=%d", tdb->track, item, chrom, start, end); sr = sqlGetResult(conn, query); if (sqlFieldColumn(sr, "bin") == 0) rowOffset = 1; while ((row = sqlNextRow(sr)) != NULL) { ++found; peptideMappingStaticLoad(row + rowOffset, &pos); if (found == 1) { printf("<B>Item:</B> %s<BR>\n", pos.name); printPos(pos.chrom, pos.chromStart, pos.chromEnd, pos.strand, TRUE, item); printf("<BR>\n"); printf("Additional details for all peptide mappings of %s:<BR>\n", item); webPrintLinkTableStart(); webPrintLabelCell("Score"); webPrintLabelCell("Raw Score"); webPrintLabelCell("Spectrum ID"); webPrintLabelCell("Peptide Rank"); } webPrintLinkTableNewRow(); webPrintIntCell(pos.score); webPrintDoubleCell(pos.rawScore); webPrintLinkCell(pos.spectrumId); webPrintIntCell(pos.peptideRank); } if (found == 0) errAbort("No items in range"); webPrintLinkTableEnd(); sqlFreeResult(&sr); /* Draw table of other locations */ printf("<BR>\n"); printf("<B>Peptide Repeat Count:</B> %d<BR>\n", pos.peptideRepeatCount); if (pos.peptideRepeatCount > 1) { struct hash *hash = hashNew(8); struct peptideMapping anotherPos; sqlSafef(query, sizeof(query), "select * from %s where name='%s' and not (chrom='%s' and chromStart=%d and chromEnd=%d)", tdb->track, item, chrom, start, end); printf("<BR>\n"); webPrintLinkTableStart(); webPrintLabelCell("Other genomic loci"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char s[1024]; peptideMappingStaticLoad(row + rowOffset, &anotherPos); char k[1024]; safef(k, sizeof k, "%s.%d.%d", anotherPos.chrom, anotherPos.chromStart, anotherPos.chromEnd); if (!hashLookup(hash, k)) { hashAdd(hash, k, NULL); safef(s, sizeof(s), "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>", hgTracksPathAndSettings(), database, anotherPos.chrom, anotherPos.chromStart+1, anotherPos.chromEnd, anotherPos.chrom, anotherPos.chromStart+1, anotherPos.chromEnd); webPrintLinkTableNewRow(); webPrintLinkCell(s); } } webPrintLinkTableEnd(); sqlFreeResult(&sr); freeHash(&hash); } }