void countChromWindows(char *database, struct scoredWindow *winList, FILE *f)
/* Go through winList and count up how many hit each chromosome. */
{
struct chromCounts *ccList = NULL, *cc;
struct hash *hash = newHash(8);
struct scoredWindow *win;
for (win = winList; win != NULL; win = win->next)
{
char *chrom = win->chrom;
cc = hashFindVal(hash, chrom);
if (cc == NULL)
{
AllocVar(cc);
slAddHead(&ccList, cc);
hashAddSaveName(hash, chrom, cc, &cc->name);
cc->chromSize = hChromSize(database, chrom);
}
cc->count += 1;
}
fprintf(f, "Finished window count per chromosome:\n");
for (cc = ccList; cc != NULL; cc = cc->next)
{
fprintf(f, "%s\t%d\t%5.2f%%\n", cc->name, cc->count,
100.0 * cc->count * bigStepSize / cc->chromSize);
}
fprintf(f, "\n");
slFreeList(&ccList);
hashFree(&hash);
}
void doOneChrom(char *database, char *chrom, char *rnaTable, char *expTable, FILE *f)
/* Process one chromosome. */
{
int chromSize = hChromSize(database, chrom);
struct binKeeper *bk = binKeeperNew(0, chromSize);
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
struct bed *exp, *rna;
int rowOffset;
struct binElement *be, *beList;
int oneCount;
/* Load up expTable into bin-keeper. */
sr = hChromQuery(conn, expTable, chrom, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
exp = bedLoadN(row + rowOffset, 12);
binKeeperAdd(bk, exp->chromStart, exp->chromEnd, exp);
}
sqlFreeResult(&sr);
/* Loop through rnaTable and look at intersections. */
sr = hChromQuery(conn, rnaTable, chrom, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
rna = bedLoadN(row + rowOffset, 12);
beList = binKeeperFind(bk, rna->chromStart, rna->chromEnd);
oneCount = 0;
for (be = beList; be != NULL; be = be->next)
{
exp = be->val;
if (exp->strand[0] == rna->strand[0])
{
++oneCount;
++hitCount;
// fprintf(f, "%s:%d-%d\t%s\t%s\n",
// rna->chrom, rna->chromStart, rna->chromEnd, rna->name, exp->name);
}
}
slFreeList(&beList);
if (oneCount == 0)
{
++missCount;
fprintf(f, "miss %s:%d-%d %c %s\n", rna->chrom, rna->chromStart, rna->chromEnd, rna->strand[0], rna->name);
}
else if (oneCount == 1)
{
fprintf(f, "uniq %s:%d-%d %c %s\n", rna->chrom, rna->chromStart, rna->chromEnd, rna->strand[0], rna->name);
++uniqCount;
}
else
{
fprintf(f, "dupe %s:%d-%d %c %s\n", rna->chrom, rna->chromStart, rna->chromEnd, rna->strand[0], rna->name);
++dupeCount;
}
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
static void loadCytoBandsIdeo(struct track *tg)
/* Load up cytoBandIdeo from database table to track items. */
{
if (tg->isBigBed)
{
struct lm *lm = lmInit(0);
int start = 0;
int end = hChromSize(database, chromName);
struct bigBedInterval *bb, *bbList = bigBedSelectRange(tg, chromName, start, end, lm);
char *bedRow[32];
char startBuf[16], endBuf[16];
for (bb = bbList; bb != NULL; bb = bb->next)
{
bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
struct cytoBand *bed = cytoBandLoad(bedRow);
slAddHead(&tg->items, bed);
}
slReverse(&tg->items);
lmCleanup(&lm);
return;
}
char query[256];
sqlSafef(query, sizeof(query),
"select * from cytoBandIdeo where chrom like '%s'", chromName);
if(hTableExists(database, "cytoBandIdeo"))
bedLoadItemByQuery(tg, "cytoBandIdeo", query, (ItemLoader)cytoBandLoad);
if(slCount(tg->items) == 0)
{
tg->limitedVisSet = TRUE;
tg->limitedVis = tvHide;
}
}
void oneTrackInit()
/* Set up global variables using cart settings and initialize libs. */
{
hPrintDisable();
database = cartUsualString(cart, "db", "ce4");
hSetDb(database);
organism = hOrganism(database);
withLeftLabels = FALSE; /* Left labels are not supported. */
withCenterLabels = cartUsualBoolean(cart, "centerLabels", FALSE);
withGuidelines = cartUsualBoolean(cart, "guidelines", FALSE);
revCmplDisp = cartUsualBooleanDb(cart, database, REV_CMPL_DISP, FALSE);
position = cartUsualString(cart, "position", "chrI:4001-5000");
hgParseChromRange(position, &chromName, &winStart, &winEnd);
insideX = 0; /* Left labels are not supported. */
insideWidth = cartUsualInt(cart, "pix", 640);
leftLabelX = 0;
leftLabelWidth = 0; /* Left labels are not supported. */
winBaseCount = winEnd - winStart;
basesPerPixel = ((float)winBaseCount) / ((float)insideWidth);
zoomedToCdsColorLevel = (winBaseCount <= insideWidth*3);
seqBaseCount = hChromSize(database, chromName);
initTl();
zoomedToBaseLevel = (winBaseCount <= insideWidth / tl.mWidth);
zoomedToCodonLevel = (ceil(winBaseCount/3) * tl.mWidth) <= insideWidth;
createHgFindMatchHash();
}
static boolean illegalCoordinate(char *db, char *chrom, int start, int end, char *line, int lineIx,
struct dyString *dyWarn)
/* verify start and end are legal for this chrom */
{
int maxEnd = hChromSize(db, chrom);
if (start < 0)
{
dyStringPrintf(dyWarn, "line %d: '%s': chromStart (%d) less than zero\n",
lineIx, line, start);
return TRUE;
}
if (end > maxEnd)
{
dyStringPrintf(dyWarn, "line %d: '%s': chromEnd (%d) greater than chrom length (%s:%d)\n",
lineIx, line, end, chrom, maxEnd);
return TRUE;
}
if (start > end)
{
dyStringPrintf(dyWarn, "line %d: '%s': chromStart (%d) greater than chromEnd (%d)\n",
lineIx, line, start, end);
return TRUE;
}
return FALSE;
}
void getBinKeeper(char *chromName)
/* put SNPs in binKeeper */
{
char query[512];
struct sqlConnection *conn = hAllocConn();
struct sqlResult *sr;
char **row;
int start = 0;
int end = 0;
char *rsId = NULL;
int chromSize = hChromSize(chromName);
verbose(1, "constructing binKeeper...\n");
snps = binKeeperNew(0, chromSize);
safef(query, sizeof(query),
"select chromStart, chromEnd, name from %s where chrom = '%s'", snpTable, chromName);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
start = sqlUnsigned(row[0]);
end = sqlUnsigned(row[1]);
rsId = cloneString(row[2]);
binKeeperAdd(snps, start, end, rsId);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
static void checkChromCoords(char *db, char *name, char *chrom, int start, int end)
/* check that bounds of a PAR are valid */
{
if (start >= end)
errAbort("zero or negative PAR length: %s %s:%d-%d", name, chrom, start, end);
if ((start < 0) || (end > hChromSize(db, chrom)))
errAbort(" PAR out of chromosome bounds: %s %s:%d-%d", name, chrom, start, end);
}
int hgSeqChromSize(char *db, char *chromName)
/* get chrom size if there's a database out there,
* otherwise just return 0 */
{
int thisSize = 0;
if (hDbExists(db))
thisSize = hChromSize(db, chromName);
return thisSize;
}
struct dnaSeq *getSkinnySeq(char *sequenceFile, char *chromName)
/* mark deletions with '-' */
{
char query[512];
struct sqlConnection *conn = hAllocConn();
struct sqlResult *sr;
char **row;
struct dnaSeq *seq;
char *seqPtr = NULL;
int pos = 0;
int start = 0;
int end = 0;
int chromSize = 0;
int snpCount = 0;
char *snpChrom = NULL;
char *rsId = NULL;
verbose(1, "sequence file = %s\n", sequenceFile);
verbose(1, "chrom = %s\n", chromName);
chromSize = hChromSize(chromName);
verbose(1, "chromSize = %d\n", chromSize);
seq = hFetchSeq(sequenceFile, chromName, 0, chromSize);
// seq = hLoadChrom(chromName);
touppers(seq->dna);
seqPtr = seq->dna;
sqlSafef(query, sizeof(query), "select chrom, chromStart, chromEnd, name from %s", snpTable);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
snpChrom = cloneString(row[0]);
start = sqlUnsigned(row[1]);
end = sqlUnsigned(row[2]);
rsId = cloneString(row[3]);
if (!sameString(snpChrom, chromName)) continue;
assert (end < chromSize);
assert (end > start);
snpCount++;
for (pos = start; pos < end; pos++)
seqPtr[pos] = '-';
}
sqlFreeResult(&sr);
hFreeConn(&conn);
if (snpCount == 0)
verbose(1, "no matching SNPs\n");
return seq;
}
void intersectOnChrom(char *db, struct sqlConnection *conn, char *chrom,
char *track1, char *track2)
/* Do intersection on one chromosome. */
{
int chromSize = hChromSize(chrom);
struct lm *lm = lmInit(0);
struct bed *bedList1, *bedList2, *andBed;
struct featureBits *fb1, *fb2;
Bits *bit1, *bit2;
int fieldCount1, fieldCount2;
struct binKeeper *bk2;
uglyTime(NULL);
scanChromTable(conn, chrom, track1);
scanChromTable(conn, chrom, track2);
uglyTime("Scan tracks");
bedList1 = getChromAsBed(conn, db, track1, chrom, lm, &fieldCount1);
bedList2 = getChromAsBed(conn, db, track2, chrom, lm, &fieldCount2);
uglyTime("Tracks as bed");
uglyf("%d items with %d fields in %s, ", slCount(bedList1), fieldCount1, track1);
uglyf("%d items with %d fields in %s\n", slCount(bedList2), fieldCount2, track2);
bit1 = bitAlloc(chromSize+8);
bit2 = bitAlloc(chromSize+8);
uglyTime("bitAlloc");
fb1 = fbList(db, chrom, track1, bedList1, chromSize);
fb2 = fbList(db, chrom, track1, bedList1, chromSize);
uglyTime("bed to featureBits list");
fbOrBits(bit1, chromSize, fb1, 0);
fbOrBits(bit2, chromSize, fb2, 0);
uglyTime("or into bits");
bitAnd(bit1, bit2, chromSize);
uglyTime("Anding bitfields");
andBed = bitsToBed4List(bit1, chromSize, chrom, 0, 0, chromSize, lm);
uglyTime("Converting bitfield to bed 4");
bitCountAllOverlaps(bedList1, bit2, fieldCount2);
uglyTime("Counting overlaps in track1 with bitfield of track2");
bk2 = fbToBinKeeper(fb2, chromSize);
uglyTime("Adding featureBits list from track 2 into binKeeper.");
bkCountAllOverlaps(bedList1, bk2, fieldCount2);
uglyTime("Count overlaps in track1 with binKeeper of track2");
featureBitsFreeList(&fb1);
featureBitsFreeList(&fb2);
uglyTime("free featureBits");
bitFree(&bit1);
bitFree(&bit2);
uglyTime("bitFree");
}
void whyConserved(char *database, char *chrom, char *homologyTrack)
/* whyConserved - Try and analyse why a particular thing is conserved. */
{
struct sqlConnection *conn;
int chromSize;
Bits *h**o = NULL;
Bits *bits = NULL;
Bits *once = NULL;
hSetDb(database);
conn = hAllocConn();
chromSize = hChromSize(chrom);
h**o = bitAlloc(chromSize);
bits = bitAlloc(chromSize);
once = bitAlloc(chromSize);
/* Get homology bitmap and set once mask to be the same. */
fbOrTableBits(h**o, homologyTrack, chrom, chromSize, conn);
bitOr(once, h**o, chromSize);
/* printHeader */
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"Track Specification", "track", "overlap",
"track", "mus", "track", "new", "cum");
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"", "size", "size",
"geno", "track", "mus", "mus", "mus");
printf("-----------------------------------------------------------------------------\n");
/* Whittle awway at homology... */
explainSome(h**o, once, bits, chrom, chromSize, conn, NULL, homologyTrack);
explainSome(h**o, once, bits, chrom, chromSize, conn, "simpleRepeat", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "rmsk", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "sanger22:CDS:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "refGene:CDS:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "sanger22:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "refGene:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "ensGene:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "rnaGene", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "mrna:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "intronEst:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "xenoMrna:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "xenoEst:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "genscan:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "genscanSubopt", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "psu:exon:10", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "sanger22:upstream:200", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "refGene:upstream:200", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "mrna:upstream:200", NULL);
explainSome(h**o, once, bits, chrom, chromSize, conn, "est", NULL);
hFreeConn(&conn);
}
static struct bed *bedTable2(struct sqlConnection *conn,
struct region *region, char *table2)
/* get a bed list, possibly complement, for table2 */
{
/* This use of bedTable rather than a bitmap is not really working. The
* rest of the table browser does intersection at the exon level, while
* the wig code, which this is part of, does it at the gene level. I
* noticed it while working on the corresponding routines for bigWig,
* which I'm building to work with bitmaps at the exon level. I'm not
* sure it's worth fixing this code since nobody has complained, and we're
* probably going to be doing mostly bigWig rather than wig in the future.
* -JK */
boolean invTable2 = cartCgiUsualBoolean(cart, hgtaInvertTable2, FALSE);
char *op = cartString(cart, hgtaIntersectOp);
struct bed *bedList = NULL;
struct lm *lm1 = lmInit(64*1024);
/* fetch table 2 as a bed list */
bedList = getFilteredBeds(conn, table2, region, lm1, NULL);
/* If table 2 bed list needs to be complemented (!table2), then do so */
if (invTable2 || sameString("none", op))
{
unsigned chromStart = 0; /* start == end == 0 */
unsigned chromEnd = 0; /* means do full chrom */
unsigned chromSize = hChromSize(database, region->chrom);
struct lm *lm2 = lmInit(64*1024);
struct bed *inverseBedList = NULL; /* new list */
if ((region->start != 0) || (region->end != 0))
{
chromStart = region->start;
chromEnd = region->end;
}
if ((struct bed *)NULL == bedList)
{
if (0 == region->end)
chromEnd = chromSize;
addBedElement(&inverseBedList, region->chrom, chromStart, chromEnd,
1, lm2);
}
else
inverseBedList=invertBedList(bedList, lm2, region->chrom, chromStart,
chromEnd, chromSize);
lmCleanup(&lm1); /* == bedFreeList(&bedList) */
return inverseBedList;
}
else
return bedList;
}
static void addPadToBed3(struct bed3 *bedList, int atStart, int atEnd)
/* Add padding to bed3 list */
{
struct bed3 *bed;
for (bed = bedList; bed != NULL; bed = bed->next)
{
int start = bed->chromStart + atStart;
if (start < 0) start = 0;
int end = bed->chromEnd + atEnd;
int chromEnd = hChromSize(database, bed->chrom);
if (end > chromEnd) end = chromEnd;
bed->chromStart = start;
bed->chromEnd = end;
}
}
static struct mafAli *mafOrAxtLoadInRegion2(struct sqlConnection *conn,struct sqlConnection *conn2,
struct trackDb *tdb, char *chrom, int start, int end,
char *axtOtherDb, char *file)
{
if (axtOtherDb != NULL)
{
struct hash *qSizeHash = hChromSizeHash(axtOtherDb);
struct mafAli *mafList = axtLoadAsMafInRegion(conn, tdb->table,
chrom, start, end, database, axtOtherDb, hChromSize(database, chrom), qSizeHash);
hashFree(&qSizeHash);
return mafList;
}
else
return mafLoadInRegion2(conn, conn2, tdb->table, chrom,
start, end, file);
}
void chromFeatureSeq(struct sqlConnection *conn,
char *database, char *chrom, char *trackSpec,
FILE *bedFile, FILE *faFile,
int *retItemCount, int *retBaseCount)
/* Write out sequence file for features from one chromosome.
* This separate routine handles the non-merged case. It's
* reason for being is so that the feature names get preserved. */
{
boolean hasBin;
char t[512], *s = NULL;
char table[HDB_MAX_TABLE_STRING];
struct featureBits *fbList = NULL, *fb;
if (trackSpec[0] == '!')
errAbort("Sorry, '!' not available with fa output unless you use faMerge");
isolateTrackPartOfSpec(trackSpec, t);
s = strchr(t, '.');
if (s != NULL)
errAbort("Sorry, only database (not file) tracks allowed with "
"fa output unless you use faMerge");
// ignore isSplit return from hFindSplitTable()
(void) hFindSplitTable(database, chrom, t, table, &hasBin);
fbList = fbGetRangeQuery(database, trackSpec, chrom, 0, hChromSize(database, chrom),
where, TRUE, TRUE);
for (fb = fbList; fb != NULL; fb = fb->next)
{
int s = fb->start, e = fb->end;
if (bedFile != NULL)
{
fprintf(bedFile, "%s\t%d\t%d\t%s",
fb->chrom, fb->start, fb->end, fb->name);
if (fb->strand != '?')
fprintf(bedFile, "\t0\t%c", fb->strand);
fprintf(bedFile, "\n");
}
if (faFile != NULL)
{
struct dnaSeq *seq = hDnaFromSeq(database, chrom, s, e, dnaLower);
if (fb->strand == '-')
reverseComplement(seq->dna, seq->size);
faWriteNext(faFile, fb->name, seq->dna, seq->size);
freeDnaSeq(&seq);
}
}
featureBitsFreeList(&fbList);
}
void chromKeeperInit(char *db)
/* Initialize the chromKeeper to a given database (hg15,mm2, etc). */
{
struct slName *names = NULL, *name = NULL;
int count=0;
names = hAllChromNames(db);
chromCount = slCount(names);
assert(chromNames == NULL && chromRanges == NULL);
AllocArray(chromNames, chromCount);
AllocArray(chromRanges, chromCount);
for(name=names; name != NULL; name = name->next)
{
int size = hChromSize(db, name->name);
chromRanges[count] = binKeeperNew(0,size);
chromNames[count] = cloneString(name->name);
count++;
}
slFreeList(&names);
}
void writeOutJobs(char *fastaFile, int size, int oligoSize, char *outDir)
{
struct slName *chromName = NULL;
char buff[512];
FILE *out = mustOpen("parasol.spec", "w");
for(chromName = chromNames; chromName != NULL; chromName = chromName->next)
{
int chromSize = hChromSize(chromName->name);
int mark = 0;
while(mark + chunkSize < chromSize)
{
fprintf(out, "nmerAlign %d %d %s%s.nib %s %s/%s:%d-%d.nmer nmerSize=%d\n",
mark, mark+chunkSize, dirName, chromName->name, fastaFile, outDir, chromName->name, mark, mark+chunkSize, oligoSize);
mark += chunkSize - 25;
}
fprintf(out, "nmerAlign %d %d %s%s.nib %s %s/%s:%d-%d.nmer nmerSize=%d\n",
mark, chromSize , dirName, chromName->name, fastaFile, outDir, chromName->name, mark, chromSize, oligoSize);
}
}
void trackOverlap(char *database, char *chrom, char *homologyTrack, char *specFile)
/* trackOverlap - Correlate a track with a series of tracks specified in specFile. */
{
struct lineFile *lf = NULL;
char *line = NULL;
struct sqlConnection *conn;
int chromSize;
Bits *h**o = NULL;
Bits *bits = NULL;
Bits *once = NULL;
lf = lineFileOpen(specFile, TRUE);
conn = hAllocConn(database);
chromSize = hChromSize(database, chrom);
h**o = bitAlloc(chromSize);
bits = bitAlloc(chromSize);
once = bitAlloc(chromSize);
/* Get homology bitmap and set once mask to be the same. */
fbOrTableBits(database, h**o, homologyTrack, chrom, chromSize, conn);
bitOr(once, h**o, chromSize);
/* printHeader */
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"Track Specification", "track", "overlap",
"track", "cov", "track", "new", "cum");
printf("%-21s %8s %8s %5s %6s %6s %5s %5s \n",
"", "size", "size",
"geno", "track", "cov", "cov", "cov");
printf("-----------------------------------------------------------------------------\n");
/* Whittle awway at homology... */
explainSome(database, h**o, once, bits, chrom, chromSize, conn, NULL, homologyTrack);
while(lineFileNextReal(lf, &line))
{
explainSome(database, h**o, once, bits, chrom, chromSize, conn, line, NULL);
}
lineFileClose(&lf);
hFreeConn(&conn);
}
static boolean illegalCoordinate(char *chrom, int start, int end)
/* verify start and end are legal for this chrom */
{
int maxEnd = hChromSize(database, chrom);
if (start < 0)
{
warn("chromStart (%d) less than zero", start);
return TRUE;
}
if (end > maxEnd)
{
warn("chromEnd (%d) greater than chrom length (%s:%d)", end, chrom, maxEnd);
return TRUE;
}
if (start >= end)
{
warn("chromStart (%d) must be less than chromEnd (%s:%d)", start, chrom, end);
return TRUE;
}
return FALSE;
}
void statsOnSpan(char *database, struct sqlConnection *conn, struct region *r,
char *axtBestDir, struct stats *stats, FILE *f,
struct scoredWindow **pWinList)
/* Gather region info on one chromosome/region. */
{
char *chrom = r->chrom;
int chromSize = hChromSize(database, chrom);
Bits *maskBits = bitAlloc(chromSize);
Bits *aliBits = bitAlloc(chromSize);
Bits *matchBits = bitAlloc(chromSize);
Bits *geneBits = bitAlloc(chromSize);
/* Set up aliBits and matchBits for to be turned on
* where bases align, and where bases align and match.
* Zero both bitmaps in areas that are transcribed. */
setAliBits(axtBestDir, chrom, chromSize, aliBits, matchBits);
maskFeatures(database, conn, chrom, chromSize, maskBits);
bitNot(maskBits, chromSize);
bitAnd(aliBits, maskBits, chromSize);
bitAnd(matchBits, maskBits, chromSize);
/* Set up maskBits to have 0's on gaps in genome */
bitClear(maskBits, chromSize);
fbOrTableBits(database, maskBits, "gap", chrom, chromSize, conn);
bitNot(maskBits, chromSize);
/* Set up bitmap for Ensemble or mRNA. */
fbOrTableBits(database, geneBits, "ensGene", chrom, chromSize, conn);
fbOrTableBits(database, geneBits, "mrna", chrom, chromSize, conn);
/* Calculate various stats on windows. */
addToStats(stats, aliBits, matchBits, geneBits, maskBits, r, f, pWinList);
/* Cleanup */
bitFree(&geneBits);
bitFree(&maskBits);
bitFree(&aliBits);
bitFree(&matchBits);
}
void mafSplitPos(char *database, char *size, char *outFile)
/* Pick best positions for split close to size.
* Use middle of a gap as preferred site.
* If not gaps are in range, use recent repeats (0% diverged) */
{
int splitSize = 0;
int chromSize = 0;
struct hash *chromHash;
struct hashCookie hc;
struct hashEl *hel;
struct sqlConnection *conn = sqlConnect(database);
FILE *f;
db = database;
verbose(1, "Finding split positions for %s at ~%s Mbp intervals\n",
database, size);
splitSize = sqlSigned(size) * 1000000;
if (chrom == NULL)
{
chromHash = hChromSizeHash(database);
}
else
{
chromHash = hashNew(6);
hashAddInt(chromHash, chrom, hChromSize(database, chrom));
}
conn = sqlConnect(database);
f = mustOpen(outFile, "w");
hc = hashFirst(chromHash);
while ((hel = hashNext(&hc)) != NULL)
{
chrom = hel->name;
chromSize = ptToInt(hel->val);
chromSplits(chrom, chromSize, splitSize, conn, f);
}
sqlDisconnect(&conn);
carefulClose(&f);
}
void eisenInput(char *database, char *outFile)
/* eisenInput - Create input for Eisen-style cluster program. */
{
struct slName *chromList = NULL, *chromEl;
FILE *f = mustOpen(outFile, "w");
char *chrom;
struct hash *refLinkHash = hashNew(0);
struct refLink *refLinkList;
struct hash *erHash = hashNew(0);
struct expRecord *erList = NULL, *er;
/* Load info good for all chromosomes. */
refLinkList = loadRefLink(database, refLinkHash);
erList = loadExpRecord(expRecordTable, "hgFixed");
for (er = erList; er != NULL; er = er->next)
{
char sid[16];
snprintf(sid, sizeof(sid), "%u", er->id);
hashAdd(erHash, sid, er);
}
/* Do it chromosome by chromosome. */
chromList = hAllChromNames(database);
for (chromEl = chromList; chromEl != NULL; chromEl = chromEl->next)
{
chrom = chromEl->name;
uglyf("%s\n", chrom);
oneChromInput(database, chrom, hChromSize(database, chrom), "rnaCluster", expTrack,
refLinkHash, erHash, f);
}
/* Cleanup time! */
expRecordFreeList(&erList);
freeHash(&erHash);
refLinkFreeList(&refLinkList);
freeHash(&refLinkHash);
}
void axtListReverse(struct axt **axtList, char *queryDb)
/* reverse complement an entire axtList */
{
struct axt *axt;
int tmp;
for (axt = *axtList; axt != NULL; axt = axt->next)
{
int qSize = 0;
if (sameString(axt->qName , "gap"))
qSize = axt->qEnd;
else
qSize = hChromSize(queryDb, axt->qName);
reverseComplement(axt->qSym, axt->symCount);
reverseComplement(axt->tSym, axt->symCount);
tmp = qSize - axt->qStart;
axt->qStart = qSize - axt->qEnd;
axt->qEnd = tmp;
}
slReverse(axtList);
}
void ultraPcrRegions(char *database, char *bedFile, char *outFa)
/* ultraPcrRegions - Get regions to PCR up and some surrounding sequence. */
{
int extraSize = 1000;
FILE *f = mustOpen(outFa, "w");
struct bed *bed, *bedList = bedLoadNAll(bedFile, 4);
hSetDb(database);
for (bed = bedList; bed != NULL; bed = bed->next)
{
int bedSize = bed->chromEnd - bed->chromStart;
int chromSize = hChromSize(bed->chrom);
int seqSize;
int seqStart = bed->chromStart - extraSize;
int seqEnd = bed->chromEnd + extraSize;
int firstParenPos, secondParenPos;
struct dyString *dy;
char fileName[512];
struct dnaSeq *seq;
if (seqStart < 0)
seqStart = 0;
if (seqEnd > chromSize)
seqEnd = chromSize;
seqSize = seqEnd - seqStart;
firstParenPos = bed->chromStart - seqStart;
secondParenPos = firstParenPos + bedSize;
seq = hChromSeqMixed(bed->chrom, seqStart, seqEnd);
dy = dyStringNew(seqSize+2);
dyStringAppendN(dy, seq->dna, firstParenPos);
dyStringAppendC(dy, '(');
dyStringAppendN(dy, seq->dna+firstParenPos, secondParenPos-firstParenPos);
dyStringAppendC(dy, ')');
dyStringAppendN(dy, seq->dna+secondParenPos, seqSize - secondParenPos);
faWriteNext(f, bed->name, dy->string, dy->stringSize);
}
carefulClose(&f);
}
void oneChrom(char *database, char *chrom, char *refAliTrack, char *bedTrack,
struct hash *otherHash, struct stats *stats)
/* Process one chromosome. */
{
struct bed *bedList = NULL, *bed;
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
int rowOffset;
int chromSize = hChromSize(database, chrom);
struct binKeeper *bk = binKeeperNew(0, chromSize);
struct psl *pslList = NULL;
struct dnaSeq *chromSeq = NULL;
if (endsWith(bedTrack, ".bed"))
{
struct lineFile *lf = lineFileOpen(bedTrack, TRUE);
char *row[3];
while (lineFileRow(lf, row))
{
if (sameString(chrom, row[0]))
{
bed = bedLoad3(row);
slAddHead(&bedList, bed);
}
}
lineFileClose(&lf);
}
else
{
sr = hChromQuery(conn, bedTrack, chrom, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoad3(row+rowOffset);
slAddHead(&bedList, bed);
}
sqlFreeResult(&sr);
}
slReverse(&bedList);
uglyf("Loaded beds\n");
sr = hChromQuery(conn, refAliTrack, chrom, NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
struct psl *psl = pslLoad(row + rowOffset);
slAddHead(&pslList, psl);
binKeeperAdd(bk, psl->tStart, psl->tEnd, psl);
}
sqlFreeResult(&sr);
uglyf("Loaded psls\n");
chromSeq = hLoadChrom(database, chrom);
/* Fetch entire chromosome into memory. */
uglyf("Loaded human seq\n");
for (bed = bedList; bed != NULL; bed = bed->next)
{
struct binElement *el, *list = binKeeperFind(bk, bed->chromStart, bed->chromEnd);
for (el = list; el != NULL; el = el->next)
{
struct psl *fullPsl = el->val;
struct psl *psl = pslTrimToTargetRange(fullPsl,
bed->chromStart, bed->chromEnd);
if (psl != NULL)
{
foldPslIntoStats(psl, chromSeq, otherHash, stats);
pslFree(&psl);
}
}
slFreeList(&list);
stats->bedCount += 1;
stats->bedBaseCount += bed->chromEnd - bed->chromStart;
sqlFreeResult(&sr);
}
freeDnaSeq(&chromSeq);
pslFreeList(&pslList);
binKeeperFree(&bk);
hFreeConn(&conn);
}
static struct bed *intersectOnRegion(
struct sqlConnection *conn, /* Open connection to database. */
struct region *region, /* Region to work inside */
char *table1, /* Table input list is from. */
struct bed *bedList1, /* List before intersection, should be
* all within region. */
struct lm *lm, /* Local memory pool. */
int *retFieldCount) /* Field count. */
/* Intersect bed list, consulting CGI vars to figure out
* with what table and how. Return intersected result,
* which is independent from input. This potentially will
* chew up bedList1. */
{
/* Grab parameters for intersection from cart. */
double moreThresh = cartCgiUsualDouble(cart, hgtaMoreThreshold, 0);
double lessThresh = cartCgiUsualDouble(cart, hgtaLessThreshold, 100);
boolean invTable = cartCgiUsualBoolean(cart, hgtaInvertTable, FALSE);
char *op = intersectOp();
/* --- TODO MIKE - replace bedList2, bits2 with baseMask stuff. */
/* Load up intersecting bedList2 (to intersect with) */
int chromSize = hChromSize(database, region->chrom);
boolean isBpWise = (sameString("and", op) || sameString("or", op));
Bits *bits2 = bitsForIntersectingTable(conn, region, chromSize, isBpWise);
/* Set up some other local vars. */
struct hTableInfo *hti1 = getHti(database, table1, conn);
struct bed *intersectedBedList = NULL;
/* Produce intersectedBedList. */
if (isBpWise)
{
/* --- TODO MIKE - replace, bits1 with baseMask stuff. */
/* Base-pair-wise operation: get bitmap for primary table too */
Bits *bits1 = bitAlloc(chromSize+8);
boolean hasBlocks = hti1->hasBlocks;
if (retFieldCount != NULL && (*retFieldCount < 12))
hasBlocks = FALSE;
bedOrBits(bits1, chromSize, bedList1, hasBlocks, 0);
/* invert inputs if necessary */
if (invTable)
bitNot(bits1, chromSize);
/* do the intersection/union */
if (sameString("and", op))
bitAnd(bits1, bits2, chromSize);
else
bitOr(bits1, bits2, chromSize);
/* clip to region if necessary: */
if (region->start > 0)
bitClearRange(bits1, 0, region->start);
if (region->end < chromSize)
bitClearRange(bits1, region->end, (chromSize - region->end));
/* translate back to bed */
intersectedBedList = bitsToBed4List(bits1, chromSize,
region->chrom, 1, region->start, region->end, lm);
if (retFieldCount != NULL)
*retFieldCount = 4;
bitFree(&bits1);
}
else
intersectedBedList = filterBedByOverlap(bedList1, hti1->hasBlocks, op,
moreThresh, lessThresh, bits2,
chromSize);
bitFree(&bits2);
return intersectedBedList;
}
struct bed *getRegionAsMergedBed(
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 subtrack-merged table.
* Cleanup result via lmCleanup(&lm) rather than bedFreeList. */
{
if (! anySubtrackMerge(db, table))
return getRegionAsBed(db, table, region, filter, idHash, lm, retFieldCount);
else
{
struct hTableInfo *hti = getHtiOnDb(database, table);
int chromSize = hChromSize(database, region->chrom);
Bits *bits1 = NULL;
Bits *bits2 = NULL;
struct bed *bedMerged = NULL;
struct trackDb *subtrack = NULL;
char *primaryType = findTypeForTable(database,curTrack,table, ctLookupName);
char *op = cartString(cart, hgtaSubtrackMergeOp);
boolean isBpWise = (sameString(op, "and") || sameString(op, "or"));
double moreThresh = cartDouble(cart, hgtaSubtrackMergeMoreThreshold);
double lessThresh = cartDouble(cart, hgtaSubtrackMergeLessThreshold);
boolean firstTime = TRUE;
if (sameString(op, "cat"))
{
struct bed *bedList = getRegionAsBed(db, table, region, filter,
idHash, lm, retFieldCount);
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(curTrack->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
subtrack = tdbRef->val;
if (! sameString(curTable, subtrack->table) &&
isSubtrackMerged(subtrack->table) &&
sameString(subtrack->type, primaryType))
{
struct bed *bedList2 =
getRegionAsBed(db, subtrack->table, region, NULL,
idHash, lm, retFieldCount);
bedList = slCat(bedList, bedList2);
}
}
slFreeList(&tdbRefList);
return bedList;
}
bits1 = bitAlloc(chromSize+8);
bits2 = bitAlloc(chromSize+8);
/* If doing a base-pair-wise operation, then start with the primary
* subtrack's ranges in bits1, and AND/OR all the selected subtracks'
* ranges into bits1. If doing a non-bp-wise intersection, then
* start with all bits clear in bits1, and then OR selected subtracks'
* ranges into bits1. */
if (isBpWise)
{
struct lm *lm2 = lmInit(64*1024);
struct bed *bedList1 = getRegionAsBed(db, table, region, filter,
idHash, lm2, retFieldCount);
bedOrBits(bits1, chromSize, bedList1, hti->hasBlocks, 0);
lmCleanup(&lm2);
}
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(curTrack->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
subtrack = tdbRef->val;
if (! sameString(curTable, subtrack->table) &&
isSubtrackMerged(subtrack->table) &&
sameString(subtrack->type, primaryType))
{
struct hTableInfo *hti2 = getHtiOnDb(database, subtrack->table);
struct lm *lm2 = lmInit(64*1024);
struct bed *bedList2 =
getRegionAsBed(db, subtrack->table, region, NULL, idHash,
lm2, NULL);
if (firstTime)
firstTime = FALSE;
else
bitClear(bits2, chromSize);
bedOrBits(bits2, chromSize, bedList2, hti2->hasBlocks, 0);
if (sameString(op, "and"))
bitAnd(bits1, bits2, chromSize);
else
bitOr(bits1, bits2, chromSize);
lmCleanup(&lm2);
}
}
slFreeList(&tdbRefList);
if (isBpWise)
{
bedMerged = bitsToBed4List(bits1, chromSize, region->chrom, 1,
region->start, region->end, lm);
if (retFieldCount != NULL)
*retFieldCount = 4;
}
else
{
struct bed *bedList1 = getRegionAsBed(db, table, region, filter,
idHash, lm, retFieldCount);
bedMerged = filterBedByOverlap(bedList1, hti->hasBlocks, op,
moreThresh, lessThresh, bits1,
chromSize);
}
bitFree(&bits1);
bitFree(&bits2);
return bedMerged;
}
}
void sortGenes(struct sqlConnection *conn)
/* Put up sort gene page. */
{
cartWebStart(cart, database, "Finding Candidate Genes for Gene Sorter");
if (!hgNearOk(database))
errAbort("Sorry, gene sorter not available for this database.");
/* Get list of regions. */
struct genoGraph *gg = ggFirstVisible();
double threshold = getThreshold();
struct bed3 *bed, *bedList = regionsOverThreshold(gg);
/* Figure out what table and column are the sorter's main gene set. */
struct hash *genomeRa = hgReadRa(genome, database, "hgNearData",
"genome.ra", NULL);
char *geneTable = hashMustFindVal(genomeRa, "geneTable");
char *idColumn = hashMustFindVal(genomeRa, "idColumn");
/* if marker labels were present when the file was uploaded, they are saved here */
char cgmName[256];
safef(cgmName, sizeof(cgmName), "%s.cgm", gg->binFileName);
struct lineFile *m = lineFileMayOpen(cgmName, TRUE);
char *cgmRow[4];
cgmRow[0] = ""; /* dummy row */
cgmRow[1] = "";
cgmRow[2] = "0";
cgmRow[3] = "0";
FILE *g = NULL;
int markerCount = 0;
struct tempName snpTn;
if (m)
{
/* Create custom column output file. */
trashDirFile(&snpTn, "hgg", "marker", ".mrk");
g = mustOpen(snpTn.forCgi, "w");
fprintf(g,
"column name=\"%s Markers\" shortLabel=\"%s Markers over threshold\" longLabel=\"%s Markers in regions over threshold\" "
"visibility=on priority=99 "
"\n"
, gg->shortLabel
, gg->shortLabel
, gg->shortLabel
);
}
/*** Build up hash of all transcriptHash that are in region. */
struct hash *transcriptHash = hashNew(16);
/* This loop handles one chromosome at a time. It depends on
* the bedList being sorted by chromosome. */
for (bed = bedList; bed != NULL; )
{
/* Make binKeeper and stuff in all regions in this chromosome into it. */
char *chrom = bed->chrom;
int chromSize = hChromSize(database, chrom);
struct binKeeper *bk = binKeeperNew(0, chromSize);
while (bed != NULL && sameString(chrom, bed->chrom))
{
binKeeperAdd(bk, bed->chromStart, bed->chromEnd, bed);
bed = bed->next;
}
struct binKeeper *bkGenes = NULL;
if (m)
bkGenes = binKeeperNew(0, chromSize);
/* Query database to find out bounds of all genes on this chromosome
* and if they overlap any of the regions then put them in the hash. */
char query[512];
safef(query, sizeof(query),
"select name,txStart,txEnd from %s where chrom='%s'", geneTable, chrom);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
while ((row = sqlNextRow(sr)) != NULL)
{
char *name = row[0];
int start = sqlUnsigned(row[1]);
int end = sqlUnsigned(row[2]);
if (binKeeperAnyOverlap(bk, start, end))
{
hashStore(transcriptHash, name);
if (m)
binKeeperAdd(bkGenes, start, end, cloneString(name));
}
}
sqlFreeResult(&sr);
if (m)
{
/* Read cgm file if it exists, looking at all markers on this chromosome
* and if they overlap any of the regions and genes then output them. */
do
{
// marker, chrom, chromStart, val
char *marker = cgmRow[0];
char *chr = cgmRow[1];
int start = sqlUnsigned(cgmRow[2]);
int end = start+1;
double val = sqlDouble(cgmRow[3]);
int cmp = strcmp(chr,chrom);
if (cmp > 0)
break;
if (cmp == 0)
{
if (val >= threshold)
{
struct binElement *el, *bkList = binKeeperFind(bkGenes, start, end);
for (el = bkList; el; el=el->next)
{
/* output to custom column trash file */
fprintf(g, "%s %s\n", (char *)el->val, marker);
}
if (bkList)
{
++markerCount;
slFreeList(&bkList);
}
}
}
}
while (lineFileRow(m, cgmRow));
}
/* Clean up for this chromosome. */
binKeeperFree(&bk);
if (m)
{
/* For speed, we do not free up the values (cloned the kg names earlier) */
binKeeperFree(&bkGenes);
}
}
/* Get list of all transcripts in regions. */
struct hashEl *el, *list = hashElListHash(transcriptHash);
/* Create file with all matching gene IDs. */
struct tempName keyTn;
trashDirFile(&keyTn, "hgg", "key", ".key");
FILE *f = mustOpen(keyTn.forCgi, "w");
for (el = list; el != NULL; el = el->next)
fprintf(f, "%s\n", el->name);
carefulClose(&f);
/* Print out some info. */
hPrintf("Thresholding <i>%s</i> at %g. ", gg->shortLabel, threshold);
hPrintf("There are %d regions covering %lld bases.<BR>\n",
slCount(bedList), bedTotalSize((struct bed*)bedList) );
hPrintf("Installed a Gene Sorter filter that selects only genes in these regions.<BR>\n");
if (m)
{
hPrintf("There are %d markers in the regions over threshold that overlap knownGenes.<BR>\n", markerCount);
hPrintf("Installed a Gene Sorter custom column called \"%s Markers\" with these markers.<BR>\n", gg->shortLabel);
}
/* close custom column output file */
if (m)
{
lineFileClose(&m);
carefulClose(&g);
}
/* Stuff cart variable with name of file. */
char keyCartName[256];
safef(keyCartName, sizeof(keyCartName), "%s%s.keyFile",
advFilterPrefix, idColumn);
cartSetString(cart, keyCartName, keyTn.forCgi);
cartSetString(cart, customFileVarName, snpTn.forCgi);
char snpVisCartNameTemp[256];
char *snpVisCartName = NULL;
safef(snpVisCartNameTemp, sizeof(snpVisCartNameTemp), "%s%s Markers.vis",
colConfigPrefix, gg->shortLabel);
snpVisCartName = replaceChars(snpVisCartNameTemp, " ", "_");
cartSetString(cart, snpVisCartName, "1");
freeMem(snpVisCartName);
hPrintf("<FORM ACTION=\"../cgi-bin/hgNear\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("<CENTER>");
cgiMakeButton("submit", "go to gene sorter");
hPrintf("</CENTER>");
hPrintf("</FORM>");
cartWebEnd();
}
void regionPicker(char *database, char *axtBestDir, char *output)
/* regionPicker - Code to pick regions to annotate deeply.. */
{
struct sqlConnection *conn = NULL;
struct slName *allChroms = NULL, *chrom = NULL;
struct region *regionList = NULL, *region;
FILE *f = mustOpen(output, "w");
struct stats *stats;
struct scoredWindow *winList = NULL;
struct hash *chromLimitHash = NULL;
AllocVar(stats);
chromLimitHash = getChromLimits(database);
/* Figure out which regions to process from command line.
* By default will do whole genome. */
if (sameWord(clRegion, "genome"))
{
allChroms = hAllChromNames(database);
for (chrom = allChroms; chrom != NULL; chrom = chrom->next)
{
if (!endsWith(chrom->name, "_random"))
{
AllocVar(region);
region->name = cloneString(chrom->name);
region->chrom = cloneString(chrom->name);
region->start = 0;
region->end = hChromSize(database, chrom->name);
slAddHead(®ionList, region);
}
}
slReverse(®ionList);
}
else if (startsWith("chr", clRegion) && strchr(clRegion, ':') == NULL)
{
AllocVar(region);
region->name = cloneString(clRegion);
region->chrom = cloneString(clRegion);
region->start = 0;
region->end = hChromSize(database, clRegion);
slAddHead(®ionList, region);
}
else
{
regionList = loadRegionFile(database, clRegion);
}
/* Gather statistics one region at a time and then
* print them. */
conn = hAllocConn(database);
for (region = regionList; region != NULL; region = region->next)
{
printf("Processing %s %s:%d-%d\n", region->name,
region->chrom, region->start, region->end);
statsOnSpan(database, conn, region, axtBestDir, stats, f, &winList);
}
fprintf(f, "\n");
reportStats(stats, f);
fprintf(f, "\n");
uglyf("Got %d windows with no gaps\n", slCount(winList));
countChromWindows(database, winList, f);
outputPicks(winList, database, chromLimitHash, stats, f);
}
void cytoBandIdeoDraw(struct track *tg,
int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw the entire chromosome with a little red box around our
current position. */
{
double scale = 0;
int xBorder = 4;
int x1, x2;
int yBorder = 0;
int chromSize = hChromSize(database, chromName);
struct cytoBand *cbList = NULL, *cb = NULL;
scale = (double) (width - (2 * xBorder)) / chromSize;
/* Subtrack 10 for the 5 pixels buffer on either side. */
tg->heightPer -= 11;
tg->lineHeight -= 11;
/* Time to draw the bands. */
hvGfxSetClip(hvg, xOff, yOff, width, tg->height);
genericDrawItems(tg, 0, chromSize, hvg, xOff+xBorder, yOff+5, width-(2*xBorder), font, color, tvDense);
x1 = round((winStart)*scale) + xOff + xBorder -1;
x2 = round((winEnd)*scale) + xOff + xBorder -1;
if(x1 >= x2)
x2 = x1+1;
yBorder = tg->heightPer + 7 + 1;
/* Draw an outline around chromosome for visualization purposes. Helps
to make the chromosome look better. */
hvGfxLine(hvg, xOff+xBorder, yOff+4, xOff+width-xBorder, yOff+4, MG_BLACK);
hvGfxLine(hvg, xOff+xBorder, yOff+yBorder-3, xOff+width-xBorder, yOff+yBorder-3, MG_BLACK);
hvGfxLine(hvg, xOff+xBorder, yOff+4, xOff+xBorder, yOff+yBorder-3, MG_BLACK);
hvGfxLine(hvg, xOff+width-xBorder, yOff+4, xOff+width-xBorder, yOff+yBorder-3, MG_BLACK);
/* Find and draw the centromere which is defined as the
two bands with gieStain "acen" */
cbList = tg->items;
for(cb = cbList; cb != NULL; cb = cb->next)
{
/* If centromere do some drawing. */
if(sameString(cb->gieStain, "acen"))
{
int cenLeft, cenRight, cenTop, cenBottom;
/* Get the coordinates of the edges of the centromere. */
cenLeft = round((cb->chromStart)*scale) + xOff + xBorder;
cenRight = round((cb->next->chromEnd)*scale) + xOff + xBorder;
cenTop = yOff+4;
cenBottom = yOff + yBorder - 3;
/* Draw centromere itself. */
hCytoBandDrawCentromere(hvg, cenLeft, cenTop, cenRight - cenLeft,
cenBottom-cenTop+1, MG_WHITE, hCytoBandCentromereColor(hvg));
break;
}
}
/* Draw a red box around all positions in windows for this chromName.
* Double thick so two pixels thick each. */
struct window *window;
for (window=windows; window; window=window->next)
{
if (!sameString(chromName, window->chromName))
continue;
x1 = round((window->winStart)*scale) + xOff + xBorder -1;
x2 = round((window->winEnd)*scale) + xOff + xBorder -1;
hvGfxBox(hvg, x1, yOff+1, x2-x1, 2, MG_RED);
hvGfxBox(hvg, x1, yOff + yBorder - 1, x2-x1, 2, MG_RED);
hvGfxBox(hvg, x1, yOff+1, 2, yBorder, MG_RED);
hvGfxBox(hvg, x2, yOff+1, 2, yBorder, MG_RED);
}
hvGfxUnclip(hvg);
/* Put back the lineHeight for the track
now that we are done spoofing tgDrawItems(). */
tg->heightPer += 11;
tg->lineHeight += 11;
}