4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/hgTables/bedList.c src/hg/hgTables/bedList.c index 4f18acf..892b560 100644 --- src/hg/hgTables/bedList.c +++ src/hg/hgTables/bedList.c @@ -1,842 +1,842 @@ /* bedList - get list of beds in region that pass filtering. */ /* Copyright (C) 2014 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "localmem.h" #include "dystring.h" #include "jksql.h" #include "cheapcgi.h" #include "trackDb.h" #include "customTrack.h" #include "hdb.h" #include "hui.h" #include "hCommon.h" #include "web.h" #include "featureBits.h" #include "portable.h" #include "hgTables.h" #include "wiggle.h" #include "correlate.h" #include "bedCart.h" #include "trashDir.h" #include "wikiTrack.h" boolean htiIsPsl(struct hTableInfo *hti) /* Return TRUE if table looks to be in psl format. */ { return sameString("tStarts", hti->startsField); } void bedSqlFieldsExceptForChrom(struct hTableInfo *hti, int *retFieldCount, char **retFields) /* Given tableInfo figure out what fields are needed to * add to a database query to have information to create * a bed. The chromosome is not one of these fields - we * assume that is already known since we're processing one * chromosome at a time. Return a comma separated (no last * comma) list of fields that can be freeMem'd, and the count * of fields (this *including* the chromosome). */ { struct dyString *fields = dyStringNew(128); int fieldCount = hTableInfoBedFieldCount(hti); dyStringPrintf(fields, "%s,%s", hti->startField, hti->endField); if (fieldCount >= 4) { if (hti->nameField[0] != 0) dyStringPrintf(fields, ",%s", hti->nameField); else /* Put in . as placeholder. */ dyStringPrintf(fields, ",'.'"); } if (fieldCount >= 5) { if (hti->scoreField[0] != 0) dyStringPrintf(fields, ",%s", hti->scoreField); else dyStringPrintf(fields, ",0"); } if (fieldCount >= 6) { if (hti->strandField[0] != 0) dyStringPrintf(fields, ",%s", hti->strandField); else dyStringPrintf(fields, ",'.'"); } if (fieldCount >= 8) { if (hti->cdsStartField[0] != 0) dyStringPrintf(fields, ",%s,%s", hti->cdsStartField, hti->cdsEndField); else dyStringPrintf(fields, ",%s,%s", hti->startField, hti->endField); } if (fieldCount >= 12) { dyStringPrintf(fields, ",%s,%s,%s", hti->countField, hti->endsSizesField, hti->startsField); } if (htiIsPsl(hti)) { /* For psl format we need to know chrom size as well * to handle reverse strand case. */ dyStringPrintf(fields, ",tSize"); } *retFieldCount = fieldCount; *retFields = dyStringCannibalize(&fields); } struct bed *bedFromRow( char *chrom, /* Chromosome bed is on. */ char **row, /* Row with other data for bed. */ int fieldCount, /* Number of fields in final bed. */ boolean isPsl, /* True if in PSL format. */ boolean isGenePred, /* True if in GenePred format. */ boolean isBedWithBlocks, /* True if BED with block list. */ boolean *pslKnowIfProtein,/* Have we figured out if psl is protein? */ boolean *pslIsProtein, /* True if we know psl is protien. */ struct lm *lm) /* Local memory pool */ /* Create bed from a database row when we already understand * the format pretty well. The bed is allocated inside of * the local memory pool lm. Generally use this in conjunction * with the results of a SQL query constructed with the aid * of the bedSqlFieldsExceptForChrom function. */ { char *strand, tStrand, qStrand; struct bed *bed; int i, blockCount; lmAllocVar(lm, bed); bed->chrom = chrom; bed->chromStart = sqlUnsigned(row[0]); bed->chromEnd = sqlUnsigned(row[1]); if (fieldCount < 4) return bed; bed->name = lmCloneString(lm, row[2]); if (fieldCount < 5) return bed; bed->score = atoi(row[3]); if (fieldCount < 6) return bed; strand = row[4]; qStrand = strand[0]; tStrand = strand[1]; if (tStrand == 0) bed->strand[0] = qStrand; else { /* psl: use XOR of qStrand,tStrand if both are given. */ if (tStrand == qStrand) bed->strand[0] = '+'; else bed->strand[0] = '-'; } if (fieldCount < 8) return bed; bed->thickStart = sqlUnsigned(row[5]); bed->thickEnd = sqlUnsigned(row[6]); if (fieldCount < 12) return bed; bed->blockCount = blockCount = sqlUnsigned(row[7]); lmAllocArray(lm, bed->blockSizes, blockCount); sqlSignedArray(row[8], bed->blockSizes, blockCount); lmAllocArray(lm, bed->chromStarts, blockCount); sqlSignedArray(row[9], bed->chromStarts, blockCount); if (isGenePred) { /* Translate end coordinates to sizes. */ for (i=0; i<bed->blockCount; ++i) bed->blockSizes[i] -= bed->chromStarts[i]; } else if (isPsl) { if (!*pslKnowIfProtein) { /* Figure out if is protein using a rather elaborate but * working test I think Angie or Brian must have figured out. */ if (tStrand == '-') { int tSize = sqlUnsigned(row[10]); *pslIsProtein = (bed->chromStart == tSize - ( 3*bed->blockSizes[bed->blockCount - 1] + bed->chromStarts[bed->blockCount - 1])); } else { *pslIsProtein = (bed->chromEnd == 3*bed->blockSizes[bed->blockCount - 1] + bed->chromStarts[bed->blockCount - 1]); } *pslKnowIfProtein = TRUE; } if (*pslIsProtein) { /* if protein then blockSizes are in protein space */ for (i=0; i<blockCount; ++i) bed->blockSizes[i] *= 3; } if (tStrand == '-') { /* psl: if target strand is '-', flip the coords. * (this is the target part of pslRc from src/lib/psl.c) */ int tSize = sqlUnsigned(row[10]); for (i=0; i<blockCount; ++i) { bed->chromStarts[i] = tSize - (bed->chromStarts[i] + bed->blockSizes[i]); } reverseInts(bed->chromStarts, bed->blockCount); reverseInts(bed->blockSizes, bed->blockCount); } } if (!isBedWithBlocks) { /* non-bed: translate absolute starts to relative starts */ for (i=0; i < bed->blockCount; i++) bed->chromStarts[i] -= bed->chromStart; } return bed; } struct bed *getRegionAsBed( char *db, char *table, /* Database and table. */ struct region *region, /* Region to get data for. */ char *filter, /* Filter to add to SQL where clause if any. */ struct hash *idHash, /* Restrict to id's in this hash if non-NULL. */ struct lm *lm, /* Where to allocate memory. */ int *retFieldCount) /* Number of fields. */ /* Return a bed list of all items in the given range in table. * Cleanup result via lmCleanup(&lm) rather than bedFreeList. */ { char *fields = NULL; struct sqlResult *sr; struct hTableInfo *hti; struct bed *bedList=NULL, *bed; char **row; int fieldCount; boolean isPsl, isGenePred, isBedWithBlocks; boolean pslKnowIfProtein = FALSE, pslIsProtein = FALSE; struct sqlConnection *conn = NULL; char *dbTable = NULL; if (isCustomTrack(table)) { struct customTrack *ct = ctLookupName(table); dbTable = ct->dbTableName; conn = hAllocConn(CUSTOM_TRASH); hti = hFindTableInfo(CUSTOM_TRASH, region->chrom, dbTable); } else { dbTable = table; struct trackDb *tdb; if(sameWord(db, database)) tdb = tdbForTrack(db, table, &fullTrackList); else tdb = hTrackDbForTrack(db, table); conn = (tdb ? hAllocConnTrack(db, tdb) : hAllocConn(db)); hti = hFindTableInfo(db, region->chrom, table); } if (hti == NULL) errAbort("Could not find table info for table %s.%s", db,table); if (isWiggle(db, table)) { bedList = getWiggleAsBed(db, table, region, filter, idHash, lm, conn); fieldCount = 4; } else { bedSqlFieldsExceptForChrom(hti, &fieldCount, &fields); isPsl = htiIsPsl(hti); isGenePred = sameString("exonEnds", hti->endsSizesField); isBedWithBlocks = ( (sameString("chromStarts", hti->startsField) || sameString("blockStarts", hti->startsField)) && sameString("blockSizes", hti->endsSizesField)); /* All beds have at least chrom,start,end. We omit the chrom * from the query since we already know it. */ sr = regionQuery(conn, dbTable, fields, region, TRUE, filter); while (sr != NULL && (row = sqlNextRow(sr)) != NULL) { /* If have a name field apply hash filter. */ if (fieldCount >= 4 && idHash != NULL) if (!hashLookup(idHash, row[2])) continue; bed = bedFromRow(region->chrom, row, fieldCount, isPsl, isGenePred, isBedWithBlocks, &pslKnowIfProtein, &pslIsProtein, lm); slAddHead(&bedList, bed); } freez(&fields); sqlFreeResult(&sr); slReverse(&bedList); } hFreeConn(&conn); if (retFieldCount) *retFieldCount = fieldCount; return(bedList); } struct bed *getFilteredBeds(struct sqlConnection *conn, char *table, struct region *region, struct lm *lm, int *retFieldCount) /* Get list of beds on single region that pass filtering. */ { boolean isTabix = FALSE; /* region may be part of a list, and the routines we call work on lists of * regions. Temporarily force region->next to NULL and restore at end. */ struct region *oldNext = region->next; struct bed *bedList = NULL; region->next = NULL; if (isBigBed(database, table, curTrack, ctLookupName)) bedList = bigBedGetFilteredBedsOnRegions(conn, database, table, region, lm, retFieldCount); else if (isLongTabixTable(table)) bedList = longTabixGetFilteredBedsOnRegions(conn, database, table, region, lm, retFieldCount); else if (isBamTable(table)) bedList = bamGetFilteredBedsOnRegions(conn, database, table, region, lm, retFieldCount); else if (isVcfTable(table, &isTabix)) bedList = vcfGetFilteredBedsOnRegions(conn, database, table, region, lm, retFieldCount, isTabix); else if (isHicTable(table)) bedList = hicGetFilteredBedsOnRegions(conn, database, table, region, lm, retFieldCount); else if (isCustomTrack(table)) bedList = customTrackGetFilteredBeds(database, table, region, lm, retFieldCount); else if (sameWord(table, WIKI_TRACK_TABLE)) bedList = wikiTrackGetFilteredBeds(table, region, lm, retFieldCount); else bedList = dbGetFilteredBedsOnRegions(conn, database, database, table, table, region, lm, retFieldCount); region->next = oldNext; return bedList; } /* Droplist menu for custom track visibility: */ char *ctVisMenu[] = { "hide", "dense", "squish", "pack", "full", }; int ctVisMenuSize = 5; char *ctVisWigMenu[] = { "hide", "dense", "full", }; int ctVisWigMenuSize = 3; void doBedOrCtOptions(char *table, struct sqlConnection *conn, boolean doCt) /* Put up form to get options on BED or custom track output. */ /* (Taken from hgText.c/doBedCtOptions) */ { char *table2 = NULL; /* For now... */ struct hTableInfo *hti = getHti(database, table, conn); char buf[256]; char *setting; htmlOpen("Output %s as %s", table, (doCt ? "Custom Track" : "BED")); if (doGalaxy()) startGalaxyForm(); else if (doGreat()) { verifyGreatAssemblies(); startGreatForm(); } else hPrintf("<FORM ACTION=\"%s\" METHOD=GET>\n", getScriptName()); cartSaveSession(cart); if (!doGreat()) { hPrintf("%s\n", "<TABLE><TR><TD>"); if (doCt) { hPrintf("%s\n", "</TD><TD>" "<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>" "Custom track</A> header: </B>"); } else { cgiMakeCheckBox(hgtaPrintCustomTrackHeaders, cartCgiUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE)); hPrintf("%s\n", "</TD><TD> <B> Include " "<A HREF=\"../goldenPath/help/customTrack.html\" TARGET=_blank>" "custom track</A> header: </B>"); } hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>name="); safef(buf, sizeof(buf), "tb_%s", hti->rootName); setting = cgiUsualString(hgtaCtName, buf); cgiMakeTextVar(hgtaCtName, setting, 16); hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>description="); safef(buf, sizeof(buf), "table browser query on %s%s%s", table, (table2 ? ", " : ""), (table2 ? table2 : "")); setting = cgiUsualString(hgtaCtDesc, buf); cgiMakeTextVar(hgtaCtDesc, setting, 50); hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>visibility="); if (isWiggle(database, table) || isBigWigTable(table)) { setting = cartCgiUsualString(cart, hgtaCtVis, ctVisWigMenu[2]); cgiMakeDropList(hgtaCtVis, ctVisWigMenu, ctVisWigMenuSize, setting); } else { setting = cartCgiUsualString(cart, hgtaCtVis, ctVisMenu[3]); cgiMakeDropList(hgtaCtVis, ctVisMenu, ctVisMenuSize, setting); } hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>url="); setting = cartCgiUsualString(cart, hgtaCtUrl, ""); cgiMakeTextVar(hgtaCtUrl, setting, 50); hPrintf("%s\n", "</TD></TR><TR><TD></TD><TD>"); hPrintf("%s\n", "</TD></TR></TABLE>"); } if (isWiggle(database, table) || isBedGraph(table) || isBigWigTable(table) ) { char *setting = NULL; hPrintf("<P> <B> Select type of data output: </B> <BR>\n"); setting = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData); cgiMakeRadioButton(hgtaCtWigOutType, outWigBed, sameString(setting, outWigBed)); hPrintf("BED format (no data value information, only position)<BR>\n"); cgiMakeRadioButton(hgtaCtWigOutType, outWigData, sameString(setting, outWigData)); hPrintf("DATA VALUE format (position and real valued data)</P>\n"); } else { cgiDown(0.9); hPrintf("<B> Create one BED record per: </B>\n"); if ((anyIntersection() && intersectionIsBpWise()) || (anySubtrackMerge(database, table) && subtrackMergeIsBpWise())) { /* The original table may have blocks/CDS, described in hti, but * that info will be lost after base pair-wise operations. So make * a temporary copy of hti with its flags tweaked: */ struct hTableInfo simplifiedHti; memcpy(&simplifiedHti, hti, sizeof(simplifiedHti)); simplifiedHti.hasBlocks = FALSE; simplifiedHti.hasCDS = FALSE; fbOptionsHtiCart(&simplifiedHti, cart); } else fbOptionsHtiCart(hti, cart); } if (doCt) { if (doGalaxy()) { /* send the action parameter with the form as well */ cgiMakeHiddenVar(hgtaDoGetCustomTrackFile, "get custom track in file"); printGalaxySubmitButtons(); } else { cgiMakeButton(hgtaDoGetCustomTrackTb, "get custom track in table browser"); hPrintf(" "); cgiMakeButton(hgtaDoGetCustomTrackFile, "get custom track in file"); hPrintf("<BR>\n"); cgiMakeButton(hgtaDoGetCustomTrackGb, "get custom track in genome browser"); } } else { if (doGalaxy()) { cgiMakeHiddenVar(hgtaDoGetBed, "get BED"); printGalaxySubmitButtons(); } else if (doGreat()) { cgiMakeHiddenVar(hgtaDoGetBed, "get BED"); printGreatSubmitButtons(); } else cgiMakeButton(hgtaDoGetBed, "get BED"); } if (!doGalaxy() && !doGreat()) { hPrintf(" "); cgiMakeButton(hgtaDoMainPage, "cancel"); hPrintf("</FORM>\n"); } cgiDown(0.9); htmlClose(); } void doOutBed(char *table, struct sqlConnection *conn) /* Put up form to select BED output format. */ { doBedOrCtOptions(table, conn, FALSE); } void doOutCustomTrack(char *table, struct sqlConnection *conn) /* Put up form to select Custom Track output format. */ { doBedOrCtOptions(table, conn, TRUE); } static struct customTrack *beginCustomTrack(char *table, int fields, boolean doCt, boolean doWigHdr, boolean doDataPoints) /* If doCt, return a new custom track object from TB cart settings and params; * if !doCt, return NULL but print out a header line. */ { char *ctName = cgiUsualString(hgtaCtName, table); char *ctDesc = cgiUsualString(hgtaCtDesc, table); char *ctUrl = cgiUsualString(hgtaCtUrl, ""); char *ctVis = cgiUsualString(hgtaCtVis, "dense"); int visNum = (int) hTvFromStringNoAbort(ctVis); struct customTrack *ctNew = NULL; if (visNum < 0) visNum = 0; if (doCt) { ctNew = newCt(ctName, ctDesc, visNum, ctUrl, fields); if (doDataPoints) { struct dyString *wigSettings = newDyString(0); struct tempName tn; trashDirFile(&tn, "ct", hgtaCtTempNamePrefix, ".wib"); ctNew->wibFile = cloneString(tn.forCgi); char *wiggleFile = cloneString(ctNew->wibFile); chopSuffix(wiggleFile); strcat(wiggleFile, ".wia"); ctNew->wigAscii = cloneString(wiggleFile); chopSuffix(wiggleFile); /* .wig file will be created upon encoding in customFactory */ /*strcat(wiggleFile, ".wig"); ctNew->wigFile = cloneString(wiggleFile); */ ctNew->wiggle = TRUE; dyStringPrintf(wigSettings, "type wiggle_0\nwibFile %s\n", ctNew->wibFile); ctNew->tdb->settings = dyStringCannibalize(&wigSettings); freeMem(wiggleFile); } } else { if (doWigHdr) hPrintf("track type=wiggle_0 name=\"%s\" description=\"%s\" " "visibility=%d url=%s \n", ctName, ctDesc, visNum, ctUrl); else hPrintf("track name=\"%s\" description=\"%s\" visibility=%d url=%s \n", ctName, ctDesc, visNum, ctUrl); } return ctNew; } boolean doGetBedOrCt(struct sqlConnection *conn, boolean doCt, boolean doCtFile, boolean redirectToGb) /* Actually output bed or custom track. Return TRUE unless no results. */ { char *db = cloneString(database); char *table = curTable; struct hTableInfo *hti = getHti(db, table, conn); struct featureBits *fbList = NULL, *fbPtr; struct customTrack *ctNew = NULL; boolean doCtHdr = (cartUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE) || doCt || doCtFile); char *ctWigOutType = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData); char *fbQual = fbOptionsToQualifier(); char fbTQ[128]; int fields = hTableInfoBedFieldCount(hti); boolean gotResults = FALSE; struct region *region, *regionList = getRegions(); boolean isBedGr = isBedGraph(curTable); boolean isBgWg = isBigWigTable(curTable); boolean needSubtrackMerge = anySubtrackMerge(database, curTable); boolean doDataPoints = FALSE; boolean isWig = isWiggle(database, table); struct wigAsciiData *wigDataList = NULL; struct dataVector *dataVectorList = NULL; boolean doRgb = bedItemRgb(hTrackDbForTrack(db, curTable)); if (!cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE) && !doCt) { textOpen(); } if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE)) fputs("#", stdout); if ((isWig || isBedGr || isBgWg) && sameString(outWigData, ctWigOutType)) doDataPoints = TRUE; for (region = regionList; region != NULL; region = region->next) { struct bed *bedList = NULL, *bed; struct lm *lm = lmInit(64*1024); struct dataVector *dv = NULL; if (isWig && doDataPoints) { if (needSubtrackMerge) { dv = wiggleDataVector(curTrack, curTable, conn, region); if (dv != NULL) slAddHead(&dataVectorList, dv); } else { int count = 0; struct wigAsciiData *wigData = NULL; struct wigAsciiData *asciiData; struct wigAsciiData *next; wigData = getWiggleAsData(conn, curTable, region); for (asciiData = wigData; asciiData; asciiData = next) { next = asciiData->next; if (asciiData->count) { slAddHead(&wigDataList, asciiData); ++count; } } slReverse(&wigDataList); } } else if (isBedGr && doDataPoints) { dv = bedGraphDataVector(curTable, conn, region); if (dv != NULL) slAddHead(&dataVectorList, dv); } else if (isBgWg && doDataPoints) { dv = bigWigDataVector(curTable, conn, region); if (dv != NULL) slAddHead(&dataVectorList, dv); } else if (isWig || isBgWg) { dv = wiggleDataVector(curTrack, curTable, conn, region); bedList = dataVectorToBedList(dv); dataVectorFree(&dv); } else if (isBedGr) { bedList = getBedGraphAsBed(conn, curTable, region); } else { bedList = cookedBedList(conn, curTable, region, lm, &fields); } /* this is a one-time only initial creation of the custom track * structure to receive the results. gotResults turns it off after * the first time. */ if (doCtHdr && !gotResults && ((bedList != NULL) || (wigDataList != NULL) || (dataVectorList != NULL))) { ctNew = beginCustomTrack(table, fields, doCt, (isWig || isBedGr || isBgWg), doDataPoints); } if (doDataPoints && (wigDataList || dataVectorList)) gotResults = TRUE; else { if ((fbQual == NULL) || (fbQual[0] == 0)) { for (bed = bedList; bed != NULL; bed = bed->next) { if (bed->name != NULL) { subChar(bed->name, ' ', '_'); if (strcmp(bed->name, "") == 0) bed->name = cloneString("."); } if (doCt) { struct bed *dupe = cloneBed(bed); /* Out of local memory. */ slAddHead(&ctNew->bedList, dupe); } else { if (doRgb) bedTabOutNitemRgb(bed, fields, stdout); else bedTabOutN(bed, fields, stdout); } gotResults = TRUE; } } else { safef(fbTQ, sizeof(fbTQ), "%s:%s", hti->rootName, fbQual); fbList = fbFromBed(db, fbTQ, hti, bedList, 0, 0, FALSE, FALSE); if (fields >= 6) fields = 6; else if (fields >= 4) fields = 4; else fields = 3; if (doCt && ctNew) { ctNew->fieldCount = fields; safef(ctNew->tdb->type, strlen(ctNew->tdb->type)+1, "bed %d", fields); } for (fbPtr=fbList; fbPtr != NULL; fbPtr=fbPtr->next) { if (fbPtr->name != NULL) { char *ptr = strchr(fbPtr->name, ' '); if (ptr != NULL) *ptr = 0; } if (doCt) { struct bed *fbBed = fbToBedOne(fbPtr); slAddHead(&ctNew->bedList, fbBed ); } else { if (fields >= 6) hPrintf("%s\t%d\t%d\t%s\t%d\t%c\n", fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name, 0, fbPtr->strand); else if (fields >= 4) hPrintf("%s\t%d\t%d\t%s\n", fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name); else hPrintf("%s\t%d\t%d\n", fbPtr->chrom, fbPtr->start, fbPtr->end); } gotResults = TRUE; } featureBitsFreeList(&fbList); } } bedList = NULL; lmCleanup(&lm); } if (!gotResults) { hPrintf(NO_RESULTS); } else if (doCt) { int wigDataSize = 0; /* Load existing custom tracks and add this new one: */ struct customTrack *ctList = getCustomTracks(); removeNamedCustom(&ctList, ctNew->tdb->table); if (doDataPoints) { if (needSubtrackMerge || isBedGr || isBgWg) { slReverse(&dataVectorList); wigDataSize = dataVectorWriteWigAscii(dataVectorList, ctNew->wigAscii, 0, NULL); // TODO: see if can make prettier wig output here that // doesn't necessarily have one value per base } else { struct wiggleDataStream *wds = NULL; /* create an otherwise empty wds so we can print out the list */ wds = wiggleDataStreamNew(); wds->ascii = wigDataList; wigDataSize = wds->asciiOut(wds, db, ctNew->wigAscii, TRUE, FALSE); #if defined(DEBUG) /* dbg */ /* allow file readability for debug */ chmod(ctNew->wigAscii, 0666); #endif wiggleDataStreamFree(&wds); } } else slReverse(&ctNew->bedList); slAddHead(&ctList, ctNew); /* Save the custom tracks out to file (overwrite the old file): */ customTracksSaveCart(db, cart, ctList); /* Put up redirect-to-browser page. */ if (redirectToGb) { char browserUrl[256]; char headerText[512]; int redirDelay = 3; safef(browserUrl, sizeof(browserUrl), "%s?%s&db=%s", hgTracksName(), cartSidUrlString(cart), database); safef(headerText, sizeof(headerText), "<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"%d;URL=%s\">", redirDelay, browserUrl); webStartHeader(cart, database, headerText, "Table Browser: %s %s: %s", hOrganism(database), freezeName, "get custom track"); if (doDataPoints) { hPrintf("There are %d data points in custom track. ", wigDataSize); } else { hPrintf("There are %d items in custom track. ", slCount(ctNew->bedList)); } hPrintf("You will be automatically redirected to the genome browser in\n" "%d seconds, or you can \n" "<A HREF=\"%s\">click here to continue</A>.\n", redirDelay, browserUrl); } } else if (doDataPoints) { if (needSubtrackMerge || isBedGr || isBgWg) { slReverse(&dataVectorList); dataVectorWriteWigAscii(dataVectorList, "stdout", 0, NULL); } else { /* create an otherwise empty wds so we can print out the list */ struct wiggleDataStream *wds = NULL; wds = wiggleDataStreamNew(); wds->ascii = wigDataList; wds->asciiOut(wds, db, "stdout", TRUE, FALSE); wiggleDataStreamFree(&wds); } } return gotResults; } void doGetBed(struct sqlConnection *conn) /* Get BED output (UI has already told us how). */ { doGetBedOrCt(conn, FALSE, FALSE, FALSE); } void doGetCustomTrackGb(struct sqlConnection *conn) /* Get Custom Track output (UI has already told us how). */ { doGetBedOrCt(conn, TRUE, FALSE, TRUE); } void doGetCustomTrackTb(struct sqlConnection *conn) /* Get Custom Track output (UI has already told us how). */ { boolean gotResults = doGetBedOrCt(conn, TRUE, FALSE, FALSE); if (gotResults) { flushCustomTracks(); initGroupsTracksTables(); doMainPage(conn); } } void doGetCustomTrackFile(struct sqlConnection *conn) /* Get Custom Track file output (UI has already told us how). */ { doGetBedOrCt(conn, FALSE, TRUE, FALSE); }