c7fe19c878fc68ef50674bbaa95a117499c27f56 jcasper Wed Jul 24 22:57:53 2019 -0700 Fixing bad loop limit, which resulted in using a NULL pointer. refs #23853 diff --git src/hg/hgTables/hic.c src/hg/hgTables/hic.c index 290444d..153dc20 100644 --- src/hg/hgTables/hic.c +++ src/hg/hgTables/hic.c @@ -1,397 +1,397 @@ /* hic - stuff to handle Hi-C stuff in table browser. */ /* Copyright (C) 2019 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "dystring.h" #include "localmem.h" #include "jksql.h" #include "cheapcgi.h" #include "cart.h" #include "web.h" #include "bed.h" #include "hdb.h" #include "trackDb.h" #include "obscure.h" #include "hmmstats.h" #include "correlate.h" #include "asParse.h" #include "bbiFile.h" #include "bigBed.h" #include "hubConnect.h" #include "trackHub.h" #include "hgTables.h" #include "asFilter.h" #include "xmlEscape.h" #include "hic.h" #include "interact.h" #include "hgConfig.h" #include "chromAlias.h" #include "hicUi.h" boolean isHicTable(char *table) /* Return TRUE if table corresponds to a hic file. */ { if (isHubTrack(table)) { struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table); return sameWord("hic", tdb->type); } else return trackIsType(database, table, curTrack, "hic", ctLookupName); } char *hicFileName(char *table, struct sqlConnection *conn) /* Return file name associated with hic. This handles differences whether it's * a custom or built-in track. Do a freeMem on returned string when done. */ { char *fileName = bigFileNameFromCtOrHub(table, conn); // NB: Not planning to do hic tracks via filenames in tables. If this changes, // add a check and a call to hicFileNameFromTable(), which will have to be written. return fileName; } struct hTableInfo *hicToHti(char *table) /* Get standard fields of hic into hti structure. */ { struct hTableInfo *hti; AllocVar(hti); hti->rootName = cloneString(table); hti->isPos= TRUE; safecpy(hti->chromField, sizeof(hti->chromField), "chrom"); safecpy(hti->startField, sizeof(hti->startField), "chromStart"); safecpy(hti->endField, sizeof(hti->endField), "chromEnd"); safecpy(hti->scoreField, sizeof(hti->scoreField), "value"); hti->type = cloneString("hic"); return hti; } struct slName *hicGetFields() /* Get fields of hic as simple name list. We represent hic with an interact structure, so * this is really just an interact as object. */ { struct asObject *as = interactAsObj(); return asColNames(as); } struct sqlFieldType *hicListFieldsAndTypes() /* Get fields of hic as list of sqlFieldType (again, this is really just the list of interact fields. */ { struct asObject *as = interactAsObj(); return sqlFieldTypesFromAs(as); } #define HIC_NUM_BUF_SIZE 4096 void hicRecordToRow(struct interact *sample, char *numBuf, char *row[INTERACT_NUM_COLS]) /* Convert samAlignment data structure to an array of strings, using numBuf to store * ascii versions of numbers temporarily */ { char *numPt = numBuf; char *numBufEnd = numBuf + HIC_NUM_BUF_SIZE; row[0] = sample->chrom; row[1] = numPt; numPt += sprintf(numPt, "%u", sample->chromStart); numPt += 1; row[2] = numPt; numPt += sprintf(numPt, "%u", sample->chromEnd); numPt += 1; row[3] = sample->name; row[4] = numPt; numPt += sprintf(numPt, "%u", sample->score); numPt += 1; row[5] = numPt; numPt += sprintf(numPt, "%f", sample->value); numPt += 1; row[6] = sample->exp; row[7] = numPt; numPt += sprintf(numPt, "%u", sample->color); numPt += 1; row[8] = sample->sourceChrom; row[9] = numPt; numPt += sprintf(numPt, "%u", sample->sourceStart); numPt += 1; row[10] = numPt; numPt += sprintf(numPt, "%u", sample->sourceEnd); numPt += 1; row[11] = sample->sourceName; row[12] = sample->sourceStrand; row[13] = sample->targetChrom; row[14] = numPt; numPt += sprintf(numPt, "%u", sample->targetStart); numPt += 1; row[15] = numPt; numPt += sprintf(numPt, "%u", sample->targetEnd); numPt += 1; row[16] = sample->targetName; row[17] = sample->targetStrand; assert(numPt < numBufEnd); } int hicCompare(const void *elem1, const void *elem2) /* Simple comparison function for sorting hic data in interact structures, * since it is not always returned in sorted order. */ { const struct interact *first = *((struct interact **)elem1); const struct interact *second = *((struct interact **)elem2); int dif = strcmp(first->chrom, second->chrom); if (dif == 0) dif = first->chromStart - second->chromStart; return dif; } void hicTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f) /* Print out selected fields from hic. If fields is NULL, then print out all fields. */ { if (f == NULL) f = stdout; /* Convert comma separated list of fields to array. */ int fieldCount = chopByChar(fields, ',', NULL, 0); char **fieldArray; AllocArray(fieldArray, fieldCount); chopByChar(fields, ',', fieldArray, fieldCount); /* Get list of all fields in hic and turn it into a hash of column indexes keyed by * column name. */ struct hash *fieldHash = hashNew(0); struct slName *field, *fieldList = hicGetFields(); int i; for (field = fieldList, i=0; field != NULL; field = field->next, ++i) { hashAddInt(fieldHash, field->name, i); } /* Create an array of column indexes corresponding to the selected field list. */ int *columnArray; AllocArray(columnArray, fieldCount); for (i=0; i<fieldCount; ++i) { columnArray[i] = hashIntVal(fieldHash, fieldArray[i]); } /* Output row of labels */ fprintf(f, "#%s", fieldArray[0]); for (i=1; i<fieldCount; ++i) fprintf(f, "\t%s", fieldArray[i]); fprintf(f, "\n"); struct asObject *as = interactAsObj(); struct asFilter *filter = NULL; if (anyFilter()) { filter = asFilterFromCart(cart, db, table, as); if (filter) { fprintf(f, "# Filtering on %d columns\n", slCount(filter->columnList)); } } /* Loop through outputting each region */ struct region *region, *regionList = getRegions(); int maxOut = bigFileMaxOutput(); char *fileName = hicFileName(table, conn); struct hicMeta *fileInfo; char *errMsg = hicLoadHeader(fileName, &fileInfo); if (errMsg != NULL) errAbort("%s", errMsg); char *norm = hicUiFetchNormalization(cart, table, fileInfo); for (region = regionList; region != NULL && (maxOut > 0); region = region->next) { struct interact *results = NULL, *result = NULL; int res = hicUiFetchResolutionAsInt(cart, table, fileInfo, region->end-region->start); char *errMsg = hicLoadData(fileInfo, res, norm, region->chrom, region->start, region->end, region->chrom, region->start, region->end, &results); if (errMsg != NULL) warn("%s", errMsg); slSort(&results, &hicCompare); char *row[INTERACT_NUM_COLS]; char numBuf[HIC_NUM_BUF_SIZE]; for (result = results; result != NULL && (maxOut > 0); result = result->next) { hicRecordToRow(result, numBuf, row); if (asFilterOnRow(filter, row)) { int i; fprintf(f, "%s", row[columnArray[0]]); for (i=1; i<fieldCount; ++i) fprintf(f, "\t%s", row[columnArray[i]]); fprintf(f, "\n"); maxOut --; } } } freeMem(fileName); if (maxOut == 0) errAbort("Reached output limit of %d data values, please make region smaller,\n\tor set a higher output line limit with the filter settings.", bigFileMaxOutput()); /* Clean up and exit. */ hashFree(&fieldHash); freeMem(fieldArray); freeMem(columnArray); } static void addFilteredBedsOnRegion(char *fileName, struct region *region, char *table, struct asFilter *filter, struct lm *bedLm, struct bed **pBedList, struct hash *idHash, int *pMaxOut) /* Add relevant beds in reverse order to pBedList */ { struct hicMeta *fileInfo = NULL; char *errMsg = hicLoadHeader(fileName, &fileInfo); if (errMsg != NULL) { warn("%s", errMsg); } else { int res = hicUiFetchResolutionAsInt(cart, table, fileInfo, region->end-region->start); char *norm = hicUiFetchNormalization(cart, table, fileInfo); struct interact *results = NULL, *result = NULL; errMsg = hicLoadData(fileInfo, res, norm, region->chrom, region->start, region->end, region->chrom, region->start, region->end, &results); if (errMsg != NULL) warn("%s", errMsg); slSort(&results, &hicCompare); char *row[INTERACT_NUM_COLS]; char numBuf[HIC_NUM_BUF_SIZE]; - for (result=results; results != NULL; result = result->next) + for (result=results; result != NULL; result = result->next) { hicRecordToRow(result, numBuf, row); if (asFilterOnRow(filter, row)) { struct bed *bed; lmAllocVar(bedLm, bed); bed->chrom = lmCloneString(bedLm, result->chrom); bed->chromStart = result->chromStart; bed->chromEnd = result->chromEnd; bed->name = NULL; slAddHead(pBedList, bed); } (*pMaxOut)--; if (*pMaxOut <= 0) break; } } } struct bed *hicGetFilteredBedsOnRegions(struct sqlConnection *conn, char *db, char *table, struct region *regionList, struct lm *lm, int *retFieldCount) /* Get list of beds from HIC, in all regions, that pass filtering. */ { int maxOut = bigFileMaxOutput(); /* Figure out hic file name get column info and filter. */ struct asObject *as = interactAsObj(); struct asFilter *filter = asFilterFromCart(cart, db, table, as); struct hash *idHash = identifierHash(db, table); /* Get beds a region at a time. */ struct bed *bedList = NULL; struct region *region; for (region = regionList; region != NULL; region = region->next) { char *fileName = hicFileName(table, conn); addFilteredBedsOnRegion(fileName, region, table, filter, lm, &bedList, idHash, &maxOut); freeMem(fileName); if (maxOut <= 0) { errAbort("Reached output limit of %d data values, please make region smaller,\n" "\tor set a higher output line limit with the filter settings.", bigFileMaxOutput()); } } slReverse(&bedList); return bedList; } void showSchemaHic(char *table, struct trackDb *tdb) /* Show schema on hic. */ { struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = hAllocConn(database); char *fileName = hicFileName(table, conn); struct asObject *as = interactAsObj(); hPrintf("<B>Database:</B> %s", database); hPrintf(" <B>Primary Table:</B> %s<br>", table); hPrintf("<B>HI-C File:</B> %s", fileName); hPrintf("<BR>\n"); hPrintf("<B>Format description:</B> %s<BR>", as->comment); hPrintf("See the <A HREF=\"%s\" target=_blank>Interact Format Specification</A> for more details on " "the interact format, which is available for output here. For details on the .hic format by " "the Aiden Lab, please see <a href=\"%s\" target=_blank>this page</a>.<BR>\n", "../goldenPath/help/interact.html", "https://www.aidenlab.org/documentation.html"); /* Put up table that describes fields. */ hTableStart(); hPrintf("<TR><TH>field</TH>"); hPrintf("<TH>description</TH> "); puts("</TR>\n"); struct asColumn *col; int colCount = 0; for (col = as->columnList; col != NULL; col = col->next) { hPrintf("<TR><TD><TT>%s</TT></TD>", col->name); hPrintf("<TD>%s</TD></TR>", col->comment); ++colCount; } hTableEnd(); /* Put up another section with sample rows. */ webNewSection("Sample Rows"); hTableStart(); /* Print field names as column headers for example */ hPrintf("<TR>"); int colIx = 0; for (col = as->columnList; col != NULL; col = col->next) { hPrintf("<TH>%s</TH>", col->name); ++colIx; } hPrintf("</TR>\n"); struct hicMeta *fileInfo = NULL; char *errMsg = hicLoadHeader(fileName, &fileInfo); if (errMsg != NULL) { warn("%s", errMsg); } else { /* Print sample lines. */ struct hash *chromAliasHash = chromAliasMakeLookupTable(database); char *chrName = fileInfo->chromNames[1]; // Skip 0, which is "All" struct chromAlias *a = hashFindVal(chromAliasHash, chrName); char *ucscChrName = NULL; if (a != NULL) ucscChrName = a->chrom; else ucscChrName = chrName; int maxRes = atoi(fileInfo->resolutions[0]); struct interact *sampleList = NULL, *sample = NULL; errMsg = hicLoadData(fileInfo, maxRes, "NONE", ucscChrName, 0, hChromSize(database, ucscChrName), ucscChrName, 0, hChromSize(database, ucscChrName), &sampleList); if (errMsg != NULL) warn("%s", errMsg); slSort(&sampleList, &hicCompare); char *row[INTERACT_NUM_COLS]; char numBuf[HIC_NUM_BUF_SIZE]; int count = 0; for (sample=sampleList; sample != NULL && count < 10; sample = sample->next, count++) { hicRecordToRow(sample, numBuf, row); hPrintf("<TR>"); for (colIx=0; colIx<colCount; ++colIx) { hPrintf("<TD>"); xmlEscapeStringToFile(row[colIx], stdout); hPrintf("</TD>"); } hPrintf("</TR>\n"); } } hTableEnd(); printTrackHtml(tdb); /* Clean up and go home. */ freeMem(fileName); hFreeConn(&conn); }