void webPopErrHandlers(void)
/* Pop warn and abort handler for errAbort(). */
{
popWarnHandler();
hDumpStackPopAbortHandler();
popAbortHandler();
}
void errCatchEnd(struct errCatch *errCatch)
/* Restore error handlers and pop self off of catching stack. */
{
popWarnHandler();
popAbortHandler();
struct errCatch **pErrCatchStack = getStack(), *errCatchStack = *pErrCatchStack;
if (errCatch != errCatchStack)
errAbort("Mismatch betweene errCatch and errCatchStack");
*pErrCatchStack = errCatch->next;
}
static void hDumpStackAbortHandler()
/* abort handle that prints stack dump then invokes the previous abort
* handler on the stack. */
{
if (!stackDumpDisabled)
{
stackDumpDisabled = TRUE;
popWarnHandler(); // remove us from the stack
dumpStack("\nStack dump:");
// continue with next abort handler
noWarnAbort();
}
}
int test(int argc, char *argv[])
{
int start, stop;
if (argc != 9 && argc != 10)
usageErr();
inName = argv[0];
cdnaName = argv[1];
chromDir = argv[2];
goodLogName = argv[3];
badLogName = argv[4];
unusualName = argv[5];
errName = argv[6];
start = atoi(argv[7]);
stop = atoi(argv[8]);
if (start >= stop)
usageErr();
if (argc == 10)
c2gName = argv[9];
inFile = mustOpen(inName, "r");
goodLogFile = mustOpen(goodLogName, "w");
badLogFile = mustOpen(badLogName, "w");
unusualFile = mustOpen(unusualName, "w");
errFile = mustOpen(errName, "w");
pushWarnHandler(reportWarning);
dnaUtilOpen();
printf("Loading chromosomes\n");
loadGenome(chromDir, &chroms, &chromNames, &chromCount);
startRedoHash();
printf("Analysing %s\n", inName);
if (weAreWeb())
htmlHorizontalLine();
analyse(start, stop);
//endRedoHash();
freeGenome(&chroms, &chromNames, chromCount);
popWarnHandler();
fclose(inFile);
fclose(goodLogFile);
fclose(badLogFile);
fclose(unusualFile);
fclose(errFile);
return 0;
}
char *checkParams(char *database, char *prefix, char *type)
/* If we don't have valid CGI parameters, quit with a Bad Request HTTP response. */
{
pushWarnHandler(htmlVaBadRequestAbort);
pushAbortHandler(htmlVaBadRequestAbort);
if(prefix == NULL || database == NULL)
errAbort("%s", "Missing prefix and/or db CGI parameter");
if (! hDbIsActive(database))
errAbort("'%s' is not a valid, active database", htmlEncode(database));
if (isNotEmpty(type) && differentString(type, ALT_OR_PATCH))
errAbort("'%s' is not a valid type", type);
char *table = NULL;
if (! sameOk(type, ALT_OR_PATCH))
{
struct sqlConnection *conn = hAllocConn(database);
table = connGeneSuggestTable(conn);
hFreeConn(&conn);
if(table == NULL)
errAbort("gene autosuggest is not supported for db '%s'", database);
}
popWarnHandler();
popAbortHandler();
return table;
}
static void vcfGenotypesDetails(struct vcfRecord *rec, struct trackDb *tdb, char **displayAls)
/* Print summary of allele and genotype frequency, plus collapsible section
* with table of genotype details. */
{
struct vcfFile *vcff = rec->file;
if (vcff->genotypeCount == 0)
return;
// Wrapper table for collapsible section:
puts("<TABLE>");
pushWarnHandler(ignoreEm);
vcfParseGenotypes(rec);
popWarnHandler();
// Tally genotypes and alleles for summary:
int refs = 0, alts = 0, unks = 0;
int refRefs = 0, refAlts = 0, altAlts = 0, gtUnk = 0, gtOther = 0, phasedGts = 0;
int i;
for (i = 0; i < vcff->genotypeCount; i++)
{
struct vcfGenotype *gt = &(rec->genotypes[i]);
if (gt->isPhased)
phasedGts++;
if (gt->hapIxA == 0)
refs++;
else if (gt->hapIxA > 0)
alts++;
else
unks++;
if (!gt->isHaploid)
{
if (gt->hapIxB == 0)
refs++;
else if (gt->hapIxB > 0)
alts++;
else
unks++;
if (gt->hapIxA == 0 && gt->hapIxB == 0)
refRefs++;
else if (gt->hapIxA == 1 && gt->hapIxB == 1)
altAlts++;
else if ((gt->hapIxA == 1 && gt->hapIxB == 0) ||
(gt->hapIxA == 0 && gt->hapIxB == 1))
refAlts++;
else if (gt->hapIxA < 0 || gt->hapIxB < 0)
gtUnk++;
else
gtOther++;
}
}
printf("<B>Genotype count:</B> %d", vcff->genotypeCount);
if (differentString(seqName, "chrY"))
printf(" (%d phased)", phasedGts);
else
printf(" (haploid)");
puts("<BR>");
int totalAlleles = refs + alts + unks;
double refAf = (double)refs/totalAlleles;
double altAf = (double)alts/totalAlleles;
printf("<B>Alleles:</B> %s: %d (%.3f%%); %s: %d (%.3f%%)",
displayAls[0], refs, 100*refAf, displayAls[1], alts, 100*altAf);
if (unks > 0)
printf("; unknown: %d (%.3f%%)", unks, 100 * (double)unks/totalAlleles);
puts("<BR>");
// Should be a better way to detect haploid chromosomes than comparison with "chrY":
if (vcff->genotypeCount > 1 && differentString(seqName, "chrY"))
{
printf("<B>Genotypes:</B> %s/%s: %d (%.3f%%); %s/%s: %d (%.3f%%); %s/%s: %d (%.3f%%)",
displayAls[0], displayAls[0], refRefs, 100*(double)refRefs/vcff->genotypeCount,
displayAls[0], displayAls[1], refAlts, 100*(double)refAlts/vcff->genotypeCount,
displayAls[1], displayAls[1], altAlts, 100*(double)altAlts/vcff->genotypeCount);
if (gtUnk > 0)
printf("; unknown: %d (%.3f%%)", gtUnk, 100*(double)gtUnk/vcff->genotypeCount);
if (gtOther > 0)
printf("; other: %d (%.3f%%)", gtOther, 100*(double)gtOther/vcff->genotypeCount);
printf("<BR>\n");
if (rec->alleleCount == 2)
{
boolean showHW = cartOrTdbBoolean(cart, tdb, VCF_SHOW_HW_VAR, FALSE);
if (showHW)
printf("<B><A HREF=\"http://en.wikipedia.org/wiki/Hardy%%E2%%80%%93Weinberg_principle\" "
"TARGET=_BLANK>Hardy-Weinberg equilibrium</A>:</B> "
"P(%s/%s) = %.3f%%; P(%s/%s) = %.3f%%; P(%s/%s) = %.3f%%<BR>",
displayAls[0], displayAls[0], 100*refAf*refAf,
displayAls[0], displayAls[1], 100*2*refAf*altAf,
displayAls[1], displayAls[1], 100*altAf*altAf);
}
}
puts("<BR>");
vcfGenotypeTable(rec, tdb->track, displayAls);
puts("</TABLE>");
}
static void cartJsonPopErrHandlers()
/* Pop warn and abort handlers for errAbort. */
{
popWarnHandler();
popAbortHandler();
}
static void vcfHapClusterDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Split samples' chromosomes (haplotypes), cluster them by center-weighted
* alpha similarity, and draw in the order determined by clustering. */
{
struct vcfFile *vcff = tg->extraUiData;
if (vcff->records == NULL)
return;
purple = hvGfxFindColorIx(hvg, 0x99, 0x00, 0xcc);
undefYellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
enum hapColorMode colorMode = getColorMode(tg->tdb);
pushWarnHandler(ignoreEm);
struct vcfRecord *rec;
for (rec = vcff->records; rec != NULL; rec = rec->next)
vcfParseGenotypes(rec);
popWarnHandler();
unsigned short gtHapCount = 0;
int nRecords = slCount(vcff->records);
int centerIx = getCenterVariantIx(tg, seqStart, seqEnd, vcff->records);
// Limit the number of variants that we compare, to keep from timing out:
// (really what we should limit is the number of distinct haplo's passed to hacTree!)
// In the meantime, this should at least be a cart var...
int maxVariantsPerSide = 50;
int startIx = max(0, centerIx - maxVariantsPerSide);
int endIx = min(nRecords, centerIx+1 + maxVariantsPerSide);
struct hacTree *ht = NULL;
unsigned short *gtHapOrder = clusterHaps(vcff, centerIx, startIx, endIx, >HapCount, &ht);
struct vcfRecord *centerRec = NULL;
int ix;
// Unlike drawing order (last drawn is on top), the first mapBox gets priority,
// so map center variant before drawing & mapping other variants!
for (rec = vcff->records, ix=0; rec != NULL; rec = rec->next, ix++)
{
if (ix == centerIx)
{
centerRec = rec;
mapBoxForCenterVariant(rec, hvg, tg, xOff, yOff, width);
break;
}
}
for (rec = vcff->records, ix=0; rec != NULL; rec = rec->next, ix++)
{
boolean isClustered = (ix >= startIx && ix < endIx);
if (ix != centerIx)
drawOneRec(rec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, isClustered, FALSE,
colorMode);
}
// Draw the center rec on top, outlined with black lines, to make sure it is very visible:
drawOneRec(centerRec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, TRUE, TRUE,
colorMode);
// Draw as much of the tree as can fit in the left label area:
int extraPixel = (colorMode == altOnlyMode) ? 1 : 0;
int hapHeight = tg->height- CLIP_PAD - 2*extraPixel;
struct yFromNodeHelper yHelper = {0, NULL, NULL};
initYFromNodeHelper(&yHelper, yOff+extraPixel, hapHeight, gtHapCount, gtHapOrder,
vcff->genotypeCount);
struct titleHelper titleHelper = { NULL, 0, 0, 0, 0, NULL, NULL };
initTitleHelper(&titleHelper, tg->track, startIx, centerIx, endIx, nRecords, vcff);
char *treeAngle = cartOrTdbString(cart, tg->tdb, VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE);
boolean drawRectangle = sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE);
drawTreeInLabelArea(ht, hvg, yOff+extraPixel, hapHeight+CLIP_PAD, &yHelper, &titleHelper,
drawRectangle);
}
void popRHandlers() {
popAbortHandler();
popWarnHandler();
}