src/hg/hgTables/gffOut.c 1.19
1.19 2010/02/05 06:48:54 angie
Fixed too-small char[] size, found by Ann w/ENCODE tracks w/giant names, RT 1621.
Index: src/hg/hgTables/gffOut.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTables/gffOut.c,v
retrieving revision 1.18
retrieving revision 1.19
diff -b -B -U 1000000 -r1.18 -r1.19
--- src/hg/hgTables/gffOut.c 16 Apr 2009 18:22:01 -0000 1.18
+++ src/hg/hgTables/gffOut.c 5 Feb 2010 06:48:54 -0000 1.19
@@ -1,274 +1,274 @@
/* gffOut - output GFF (from bed data structures). */
#include "common.h"
#include "hash.h"
#include "linefile.h"
#include "dystring.h"
#include "obscure.h"
#include "jksql.h"
#include "trackDb.h"
#include "bed.h"
#include "hdb.h"
#include "gff.h"
#include "hgTables.h"
static char const rcsid[] = "$Id$";
static void addGffLineFromBed(struct gffLine **pGffList, struct bed *bed,
char *source, char *feature,
int start, int end, char frame, char *txName)
/* Create a gffLine from a bed and line-specific parameters, add to list. */
{
struct gffLine *gff;
char strand;
AllocVar(gff);
gff->seq = cloneString(bed->chrom);
gff->source = cloneString(source);
gff->feature = cloneString(feature);
gff->start = start;
gff->end = end;
gff->score = bed->score;
strand = bed->strand[0];
if (strand != '+' && strand != '-')
strand = '.';
gff->strand = strand;
gff->frame = frame;
gff->group = cloneString(txName);
if (bed->name != NULL)
gff->geneId = cloneString(bed->name);
else
{
static int namelessIx = 0;
char buf[64];
safef(buf, sizeof(buf), "gene%d", ++namelessIx);
gff->geneId = cloneString(buf);
}
slAddHead(pGffList, gff);
}
static void addCdsStartStop(struct gffLine **pGffList, struct bed *bed,
char *source, int s, int e, char *frames,
int i, int startIndx, int stopIndx,
boolean gtf2StopCodons, char *txName)
{
/* start_codon (goes first for + strand) overlaps with CDS */
if ((i == startIndx) && (bed->strand[0] != '-'))
{
addGffLineFromBed(pGffList, bed, source, "start_codon",
s, s+3, '.', txName);
}
/* stop codon does not overlap with CDS as of GTF2 */
if ((i == stopIndx) && gtf2StopCodons)
{
if (bed->strand[0] == '-')
{
addGffLineFromBed(pGffList, bed, source, "stop_codon",
s, s+3, '.', txName);
addGffLineFromBed(pGffList, bed, source, "CDS", s+3, e,
frames[i], txName);
}
else
{
addGffLineFromBed(pGffList, bed, source, "CDS", s, e-3,
frames[i], txName);
addGffLineFromBed(pGffList, bed, source, "stop_codon",
e-3, e, '.', txName);
}
}
else
{
addGffLineFromBed(pGffList, bed, source, "CDS", s, e,
frames[i], txName);
}
/* start_codon (goes last for - strand) overlaps with CDS */
if ((i == startIndx) && (bed->strand[0] == '-'))
{
addGffLineFromBed(pGffList, bed, source, "start_codon",
e-3, e, '.', txName);
}
}
struct gffLine *bedToGffLines(struct bed *bedList, struct hTableInfo *hti,
int fieldCount, char *source, boolean gtf2StopCodons)
/* Translate a (list of) bed into list of gffLine elements.
* Note that field count (perhaps reduced by bitwise intersection)
* can in effect override hti. */
{
struct hash *nameHash = newHash(20);
struct gffLine *gffList = NULL;
struct bed *bed;
int i, j, s, e;
char txName[256];
static int namelessIx = 0;
for (bed = bedList; bed != NULL; bed = bed->next)
{
/* Enforce unique transcript_ids. */
if (bed->name != NULL)
{
struct hashEl *hel = hashLookup(nameHash, bed->name);
int dupCount = (hel != NULL ? ptToInt(hel->val) : 0);
if (dupCount > 0)
{
safef(txName, sizeof(txName), "%s_dup%d", bed->name, dupCount);
hel->val = intToPt(dupCount + 1);
}
else
{
safef(txName, sizeof(txName), "%s", bed->name);
hashAddInt(nameHash, bed->name, 1);
}
}
else
{
safef(txName, sizeof(txName), "tx%d\n", ++namelessIx);
}
if (hti->hasBlocks && hti->hasCDS && fieldCount > 4)
{
char *frames = needMem(bed->blockCount);
boolean gotFirstCds = FALSE;
int nextPhase = 0;
int startIndx = 0;
int stopIndx = 0;
if (bed->thickStart == 0 && bed->thickEnd == 0)
bed->thickStart = bed->thickEnd = bed->chromStart;
/* first pass: compute frames, in order dictated by strand. */
for (i=0; i < bed->blockCount; i++)
{
if (bed->strand[0] == '-')
j = bed->blockCount-i-1;
else
j = i;
s = bed->chromStart + bed->chromStarts[j];
e = s + bed->blockSizes[j];
if ((s < bed->thickEnd) && (e > bed->thickStart))
{
int cdsSize = e - s;
if (e > bed->thickEnd)
cdsSize = bed->thickEnd - s;
else if (s < bed->thickStart)
cdsSize = e - bed->thickStart;
if (! gotFirstCds)
{
gotFirstCds = TRUE;
startIndx = j;
}
frames[j] = '0' + nextPhase;
nextPhase = (3 + ((nextPhase - cdsSize) % 3)) % 3;
stopIndx = j;
}
else
{
frames[j] = '.';
}
}
/* second pass: one exon (possibly CDS, start/stop_codon) per block. */
for (i=0; i < bed->blockCount; i++)
{
s = bed->chromStart + bed->chromStarts[i];
e = s + bed->blockSizes[i];
if ((s >= bed->thickStart) && (e <= bed->thickEnd))
{
addCdsStartStop(&gffList, bed, source, s, e, frames,
i, startIndx, stopIndx, gtf2StopCodons,
txName);
}
else if ((s < bed->thickStart) && (e > bed->thickEnd))
{
addCdsStartStop(&gffList, bed, source,
bed->thickStart, bed->thickEnd,
frames, i, startIndx, stopIndx,
gtf2StopCodons, txName);
}
else if ((s < bed->thickStart) && (e > bed->thickStart))
{
addCdsStartStop(&gffList, bed, source, bed->thickStart, e,
frames, i, startIndx, stopIndx,
gtf2StopCodons, txName);
}
else if ((s < bed->thickEnd) && (e > bed->thickEnd))
{
addCdsStartStop(&gffList, bed, source, s, bed->thickEnd,
frames, i, startIndx, stopIndx,
gtf2StopCodons, txName);
}
addGffLineFromBed(&gffList, bed, source, "exon", s, e, '.',
txName);
}
freeMem(frames);
}
else if (hti->hasBlocks && fieldCount > 4)
{
for (i=0; i < bed->blockCount; i++)
{
s = bed->chromStart + bed->chromStarts[i];
e = s + bed->blockSizes[i];
addGffLineFromBed(&gffList, bed, source, "exon", s, e, '.',
txName);
}
}
else if (hti->hasCDS && fieldCount > 4)
{
if (bed->thickStart == 0 && bed->thickEnd == 0)
bed->thickStart = bed->thickEnd = bed->chromStart;
if (bed->thickStart > bed->chromStart)
{
addGffLineFromBed(&gffList, bed, source, "exon", bed->chromStart,
bed->thickStart, '.', txName);
}
if (bed->thickEnd > bed->thickStart)
addGffLineFromBed(&gffList, bed, source, "CDS", bed->thickStart,
bed->thickEnd, '0', txName);
if (bed->thickEnd < bed->chromEnd)
{
addGffLineFromBed(&gffList, bed, source, "exon", bed->thickEnd,
bed->chromEnd, '.', txName);
}
}
else
{
addGffLineFromBed(&gffList, bed, source, "exon", bed->chromStart,
bed->chromEnd, '.', txName);
}
}
slReverse(&gffList);
hashFree(&nameHash);
return(gffList);
}
void doOutGff(char *table, struct sqlConnection *conn)
/* Save as GFF. */
{
struct hTableInfo *hti = getHti(database, table, conn);
struct bed *bedList;
struct gffLine *gffList, *gffPtr;
-char source[64];
+char source[HDB_MAX_TABLE_STRING];
int itemCount;
boolean gtf2StopCodons = FALSE;
struct region *region, *regionList = getRegions();
textOpen();
safef(source, sizeof(source), "%s_%s", database, table);
itemCount = 0;
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(64*1024);
int fieldCount;
bedList = cookedBedList(conn, table, region, lm, &fieldCount);
gffList = bedToGffLines(bedList, hti, fieldCount, source, gtf2StopCodons);
bedList = NULL;
lmCleanup(&lm);
for (gffPtr = gffList; gffPtr != NULL; gffPtr = gffPtr->next)
{
gffTabOut(gffPtr, stdout);
itemCount++;
}
slFreeList(&gffList);
}
if (itemCount == 0)
hPrintf(NO_RESULTS);
}