コード例 #1
0
ファイル: bigBed.c プロジェクト: Nicholas-NVS/kentUtils
struct bed *bigBedGetFilteredBedsOnRegions(struct sqlConnection *conn,
	char *db, char *table, struct region *regionList, struct lm *lm,
	int *retFieldCount)
/* Get list of beds from bigBed, in all regions, that pass filtering. */
{
/* Connect to big bed and get metadata and filter. */
char *fileName = bigBedFileName(table, conn);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct asObject *as = bigBedAsOrDefault(bbi);
struct asFilter *filter = asFilterFromCart(cart, db, table, as);

/* Get beds a region at a time. */
struct bed *bedList = NULL;
struct region *region;
for (region = regionList; region != NULL; region = region->next)
    addFilteredBedsOnRegion(bbi, region, table, filter, lm, &bedList);
slReverse(&bedList);

/* Clean up and return. */
if (retFieldCount != NULL)
	*retFieldCount = bbi->definedFieldCount;
bbiFileClose(&bbi);
freeMem(fileName);
return bedList;
}
コード例 #2
0
ファイル: bam.c プロジェクト: maximilianh/kent
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;
}
コード例 #3
0
ファイル: bigBed.c プロジェクト: Nicholas-NVS/kentUtils
void bigBedTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f)
/* Print out selected fields from Big Bed.  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 big bed and turn it into a hash of column indexes keyed by
 * column name. */
struct hash *fieldHash = hashNew(0);
struct slName *bb, *bbList = bigBedGetFields(table, conn);
int i;
for (bb = bbList, i=0; bb != NULL; bb = bb->next, ++i)
    hashAddInt(fieldHash, bb->name, i);

// If bigBed has name column, look up pasted/uploaded identifiers if any:
struct hash *idHash = NULL;
if (slCount(bbList) >= 4)
    idHash = identifierHash(db, table);

/* 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");

/* Open up bigBed file. */
char *fileName = bigBedFileName(table, conn);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct asObject *as = bigBedAsOrDefault(bbi);
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();
for (region = regionList; region != NULL; region = region->next)
    {
    struct lm *lm = lmInit(0);
    struct bigBedInterval *iv, *ivList = bigBedIntervalQuery(bbi, region->chrom,
    	region->start, region->end, 0, lm);
    char *row[bbi->fieldCount];
    char startBuf[16], endBuf[16];
    for (iv = ivList; iv != NULL; iv = iv->next)
        {
	bigBedIntervalToRow(iv, region->chrom, startBuf, endBuf, row, bbi->fieldCount);
	if (asFilterOnRow(filter, row))
	    {
	    if ((idHash != NULL) && (hashLookup(idHash, row[3]) == 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");
	    }
	}
    lmCleanup(&lm);
    }

/* Clean up and exit. */
bbiFileClose(&bbi);
hashFree(&fieldHash);
freeMem(fieldArray);
freeMem(columnArray);
}
コード例 #4
0
ファイル: bam.c プロジェクト: maximilianh/kent
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();
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);
}
コード例 #5
0
ファイル: vcf.c プロジェクト: Nicholas-NVS/kentUtils
void vcfTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f,
	       boolean isTabix)
/* Print out selected fields from VCF.  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 = vcfGetFields();
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]);
    }

// If we are outputting a subset of fields, invalidate the VCF header.
boolean allFields = (fieldCount == VCFDATALINE_NUM_COLS);
if (!allFields)
    fprintf(f, "# Only selected columns are included below; output is not valid VCF.\n");

struct asObject *as = vcfAsObj();
struct asFilter *filter = NULL;
if (anyFilter())
    filter = asFilterFromCart(cart, db, table, as);

/* Loop through outputting each region */
struct region *region, *regionList = getRegions();
int maxOut = bigFileMaxOutput();
struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table);
// Include the header, absolutely necessary for VCF parsing.
boolean printedHeader = FALSE;
// Temporary storage for row-ification:
struct dyString *dyAlt = newDyString(1024);
struct dyString *dyFilter = newDyString(1024);
struct dyString *dyInfo = newDyString(1024);
struct dyString *dyGt = newDyString(1024);
struct vcfRecord *rec;
for (region = regionList; region != NULL && (maxOut > 0); region = region->next)
    {
    char *fileName = vcfFileName(tdb, conn, table, region->chrom);
    struct vcfFile *vcff;
    if (isTabix)
	vcff = vcfTabixFileMayOpen(fileName, region->chrom, region->start, region->end,
				   100, maxOut);
    else
	vcff = vcfFileMayOpen(fileName, region->chrom, region->start, region->end,
			      100, maxOut, TRUE);
    if (vcff == NULL)
	noWarnAbort();
    // If we are outputting all fields, but this VCF has no genotype info, omit the
    // genotype columns from output:
    if (allFields && vcff->genotypeCount == 0)
	fieldCount = VCFDATALINE_NUM_COLS - 2;
    if (!printedHeader)
	{
	fprintf(f, "%s", vcff->headerString);
	if (filter)
	    fprintf(f, "# Filtering on %d columns\n", slCount(filter->columnList));
	if (!allFields)
	    {
	    fprintf(f, "#%s", fieldArray[0]);
	    for (i=1; i<fieldCount; ++i)
		fprintf(f, "\t%s", fieldArray[i]);
	    fprintf(f, "\n");
	    }
	printedHeader = TRUE;
	}
    char *row[VCFDATALINE_NUM_COLS];
    char numBuf[VCF_NUM_BUF_SIZE];
    for (rec = vcff->records;  rec != NULL && (maxOut > 0);  rec = rec->next)
        {
	vcfRecordToRow(rec, region->chrom, numBuf, dyAlt, dyFilter, dyInfo, dyGt, row);
	if (asFilterOnRow(filter, row))
	    {
	    /* if we're looking for identifiers, check if this matches */
	    if ((idHash != NULL) && (hashLookup(idHash, row[idFieldNum]) == NULL))
		continue;
	    // All fields output: after asFilter'ing, preserve original VCF chrom
	    if (allFields && !sameString(rec->chrom, region->chrom))
		row[0] = rec->chrom;
	    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 --;
	    }
	}
    vcfFileFree(&vcff);
    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());
/* Clean up and exit. */
dyStringFree(&dyAlt);  dyStringFree(&dyFilter);  dyStringFree(&dyInfo);  dyStringFree(&dyGt);
hashFree(&fieldHash);
freeMem(fieldArray);
freeMem(columnArray);
}