0522c607db08f0b12624eb6187fedf714b427243 kent Mon Mar 19 14:20:20 2012 -0700 Making this escape '<' and '>' tags and the like better. diff --git src/hg/hgTables/bam.c src/hg/hgTables/bam.c index 346bdea..8117251 100644 --- src/hg/hgTables/bam.c +++ src/hg/hgTables/bam.c @@ -1,401 +1,404 @@ /* bam - stuff to handle BAM stuff in table browser. */ #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 "hgTables.h" #include "asFilter.h" +#include "xmlEscape.h" #include "hgBam.h" #if (defined USE_BAM && defined KNETFILE_HOOKS) #include "knetUdc.h" #include "udc.h" #endif//def USE_BAM && KNETFILE_HOOKS boolean isBamTable(char *table) /* Return TRUE if table corresponds to a BAM file. */ { if (isHubTrack(table)) { struct trackDb *tdb = hashFindVal(fullTrackAndSubtrackHash, table); return startsWithWord("bam", tdb->type); } else return trackIsType(database, table, curTrack, "bam", ctLookupName); } char *bamFileName(char *table, struct sqlConnection *conn, char *seqName) /* Return file name associated with BAM. 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); if (fileName == NULL) fileName = bamFileNameFromTable(conn, table, seqName); return fileName; } struct hTableInfo *bamToHti(char *table) /* Get standard fields of BAM into hti structure. */ { struct hTableInfo *hti; AllocVar(hti); hti->rootName = cloneString(table); hti->isPos= TRUE; strcpy(hti->chromField, "rName"); strcpy(hti->startField, "pos"); strcpy(hti->nameField, "qName"); hti->type = cloneString("bam"); return hti; } struct slName *bamGetFields(char *table) /* Get fields of bam as simple name list. */ { struct asObject *as = bamAsObj(); return asColNames(as); } struct sqlFieldType *bamListFieldsAndTypes() /* Get fields of bigBed as list of sqlFieldType. */ { struct asObject *as = bamAsObj(); return sqlFieldTypesFromAs(as); } #define BAM_NUM_BUF_SIZE 256 void samAlignmentToRow(struct samAlignment *sam, char *numBuf, char *row[SAMALIGNMENT_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 + BAM_NUM_BUF_SIZE; row[0] = sam->qName; row[1] = numPt; numPt += sprintf(numPt, "%u", sam->flag); numPt += 1; row[2] = sam->rName; row[3] = numPt; numPt += sprintf(numPt, "%u", sam->pos); numPt += 1; row[4] = numPt; numPt += sprintf(numPt, "%u", sam->mapQ); numPt += 1; row[5] = sam->cigar; row[6] = sam->rNext; row[7] = numPt; numPt += sprintf(numPt, "%d", sam->pNext); numPt += 1; row[8] = numPt; numPt += sprintf(numPt, "%d", sam->tLen); numPt += 1; row[9] = sam->seq; row[10] = sam->qual; row[11] = sam->tagTypeVals; assert(numPt < numBufEnd); } void bamTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f) /* Print out selected fields from BAM. If fields is NULL, then print out all fields. */ { struct hTableInfo *hti = NULL; hti = getHti(db, table, conn); struct hash *idHash = NULL; char *idField = getIdField(db, curTrack, table, hti); int idFieldNum = 0; /* if we know what field to use for the identifiers, get the hash of names */ if (idField != NULL) idHash = identifierHash(db, table); 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 big bed and turn it into a hash of column indexes keyed by * column name. */ struct hash *fieldHash = hashNew(0); struct slName *bb, *bbList = bamGetFields(table); int i; for (bb = bbList, i=0; bb != NULL; bb = bb->next, ++i) { /* if we know the field for identifiers, save it away */ if ((idField != NULL) && sameString(idField, bb->name)) idFieldNum = i; hashAddInt(fieldHash, bb->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 = bamAsObj(); 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(); for (region = regionList; region != NULL && (maxOut > 0); region = region->next) { struct lm *lm = lmInit(0); char *fileName = bamFileName(table, conn, region->chrom); struct samAlignment *sam, *samList = bamFetchSamAlignment(fileName, region->chrom, region->start, region->end, lm); char *row[SAMALIGNMENT_NUM_COLS]; char numBuf[BAM_NUM_BUF_SIZE]; for (sam = samList; sam != NULL && (maxOut > 0); sam = sam->next) { samAlignmentToRow(sam, numBuf, row); if (asFilterOnRow(filter, row)) { /* if we're looking for identifiers, check if this matches */ if ((idHash != NULL)&&(hashLookup(idHash, row[idFieldNum]) == NULL)) continue; 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); lmCleanup(&lm); } if (maxOut == 0) warn("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); } int cigarWidth(char *cigar, int cigarSize) /* Return width of alignment as encoded in cigar format string. */ { int tLength=0; char *s, *end = cigar + cigarSize; s = cigar; while (s < end) { int digCount = countLeadingDigits(s); if (digCount <= 0) errAbort("expecting number got %s in cigarWidth", s); int n = atoi(s); s += digCount; char op = *s++; switch (op) { case 'M': // match or mismatch (gapless aligned block) tLength += n; break; case 'I': // inserted in query break; case 'D': // deleted from query case 'N': // long deletion from query (intron as opposed to small del) tLength += n; break; case 'S': // skipped query bases at beginning or end ("soft clipping") case 'H': // skipped query bases not stored in record's query sequence ("hard clipping") case 'P': // P="silent deletion from padded reference sequence" -- ignore these. break; default: errAbort("cigarWidth: unrecognized CIGAR op %c -- update me", op); } } return tLength; } 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 lm *lm = lmInit(0); struct samAlignment *sam, *samList = bamFetchSamAlignment(fileName, region->chrom, region->start, region->end, lm); char *row[SAMALIGNMENT_NUM_COLS]; char numBuf[BAM_NUM_BUF_SIZE]; for (sam = samList; sam != NULL; sam = sam->next) { samAlignmentToRow(sam, numBuf, row); if (asFilterOnRow(filter, row)) { if ((idHash != NULL) && (hashLookup(idHash, sam->qName) == NULL)) continue; struct bed *bed; lmAllocVar(bedLm, bed); bed->chrom = lmCloneString(bedLm, sam->rName); bed->chromStart = sam->pos - 1; bed->chromEnd = bed->chromStart + cigarWidth(sam->cigar, strlen(sam->cigar)); bed->name = lmCloneString(bedLm, sam->qName); slAddHead(pBedList, bed); } (*pMaxOut)--; if (*pMaxOut <= 0) break; } lmCleanup(&lm); } struct bed *bamGetFilteredBedsOnRegions(struct sqlConnection *conn, char *db, char *table, struct region *regionList, struct lm *lm, int *retFieldCount) /* Get list of beds from BAM, in all regions, that pass filtering. */ { int maxOut = bigFileMaxOutput(); /* Figure out bam file name get column info and filter. */ struct asObject *as = bamAsObj(); 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 = bamFileName(table, conn, region->chrom); addFilteredBedsOnRegion(fileName, region, table, filter, lm, &bedList, idHash, &maxOut); freeMem(fileName); if (maxOut <= 0) { warn("Reached output limit of %d data values, please make region smaller,\n" "\tor set a higher output line limit with the filter settings.", bigFileMaxOutput()); break; } } slReverse(&bedList); return bedList; } struct slName *randomBamIds(char *table, struct sqlConnection *conn, int count) /* Return some semi-random qName based IDs from a BAM file. */ { /* Read 10000 items from bam file, or if they ask for a big list, then 4x what they ask for. */ char *fileName = bamFileName(table, conn, NULL); samfile_t *fh = bamOpen(fileName, NULL); struct lm *lm = lmInit(0); int orderedCount = count * 4; if (orderedCount < 10000) orderedCount = 10000; struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, orderedCount, lm); /* Shuffle list and extract qNames from first count of them. */ shuffleList(&samList, 1); struct slName *randomIdList = NULL; int i; for (i=0, sam = samList; i<count && sam != NULL; ++i, sam = sam->next) slNameAddHead(&randomIdList, sam->qName); /* Clean up and go home. */ lmCleanup(&lm); bamClose(&fh); freez(&fileName); return randomIdList; } void showSchemaBam(char *table) /* Show schema on bam. */ { struct sqlConnection *conn = hAllocConn(database); char *fileName = bamFileName(table, conn, NULL); struct asObject *as = bamAsObj(); hPrintf("<B>Database:</B> %s", database); hPrintf(" <B>Primary Table:</B> %s<br>", table); hPrintf("<B>BAM File:</B> %s", fileName); hPrintf("<BR>\n"); hPrintf("<B>Format description:</B> %s<BR>", as->comment); hPrintf("See the <A HREF=\"%s\" target=_blank>SAM Format Specification</A> for more details<BR>\n", "http://samtools.sourceforge.net/SAM1.pdf"); /* 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"); /* Fetch sample rows. */ samfile_t *fh = bamOpen(fileName, NULL); struct lm *lm = lmInit(0); struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, 10, lm); /* Print sample lines. */ char *row[SAMALIGNMENT_NUM_COLS]; char numBuf[BAM_NUM_BUF_SIZE]; for (sam=samList; sam != NULL; sam = sam->next) { samAlignmentToRow(sam, numBuf, row); hPrintf("<TR>"); for (colIx=0; colIx<colCount; ++colIx) { - writeHtmlCell(row[colIx]); + hPrintf("<TD>"); + xmlEscapeStringToFile(row[colIx], stdout); + hPrintf("</TD>"); } hPrintf("</TR>\n"); } hTableEnd(); /* Clean up and go home. */ bamClose(&fh); lmCleanup(&lm); freeMem(fileName); hFreeConn(&conn); }