void mapBoxForCenterVariant(struct vcfRecord *rec, struct hvGfx *hvg, struct track *tg,
int xOff, int yOff, int width)
/* Special mouseover for center variant */
{
struct dyString *dy = dyStringNew(0);
unsigned int chromStartMap = vcfRecordTrimIndelLeftBase(rec);
unsigned int chromEndMap = vcfRecordTrimAllelesRight(rec);
gtSummaryString(rec, dy);
dyStringAppend(dy, " Haplotypes sorted on ");
char *centerChrom = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "centerVariantChrom");
if (centerChrom == NULL || !sameString(chromName, centerChrom))
dyStringAppend(dy, "middle variant by default. ");
else
dyStringAppend(dy, "this variant. ");
dyStringAppend(dy, "To anchor sorting to a different variant, click on that variant and "
"then click on the 'Use this variant' button below the variant name.");
const double scale = scaleForPixels(width);
int x1 = round((double)(rec->chromStart-winStart)*scale) + xOff;
int x2 = round((double)(rec->chromEnd-winStart)*scale) + xOff;
int w = x2-x1;
if (w <= 1)
{
x1--;
w = 3;
}
mapBoxHgcOrHgGene(hvg, chromStartMap, chromEndMap, x1, yOff, w, tg->height, tg->track,
rec->name, dy->string, NULL, TRUE, NULL);
}
static void vcfRecordDetails(struct trackDb *tdb, struct vcfRecord *rec)
/* Display the contents of a single line of VCF, assumed to be from seqName
* (using seqName instead of rec->chrom because rec->chrom might lack "chr"). */
{
printf("<B>Name:</B> %s<BR>\n", rec->name);
// Since these are variants, if it looks like a dbSNP or dbVar ID, provide a link:
if (regexMatch(rec->name, "^rs[0-9]+$"))
{
printf("<B>dbSNP:</B> ");
printDbSnpRsUrl(rec->name, "%s", rec->name);
puts("<BR>");
}
else if (regexMatch(rec->name, "^[en]ss?v[0-9]+$"))
{
printf("<B>dbVar:</B> ");
printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" "
"TARGET=_BLANK>%s</A><BR>\n", rec->name, rec->name);
}
printCustomUrl(tdb, rec->name, TRUE);
boolean hapClustEnabled = cartOrTdbBoolean(cart, tdb, VCF_HAP_ENABLED_VAR, TRUE);
if (hapClustEnabled)
{
static char *formName = "vcfCfgHapCenter";
printf("<FORM NAME=\"%s\" ACTION=\"%s\">\n", formName, hgTracksName());
cartSaveSession(cart);
vcfCfgHaplotypeCenter(cart, tdb, tdb->track, FALSE, rec->file, rec->name,
seqName, rec->chromStart, formName);
printf("</FORM>\n");
}
char leftBase = rec->alleles[0][0];
unsigned int vcfStart = vcfRecordTrimIndelLeftBase(rec);
boolean showLeftBase = (rec->chromStart == vcfStart+1);
(void)vcfRecordTrimAllelesRight(rec);
char *displayAls[rec->alleleCount];
makeDisplayAlleles(rec, showLeftBase, leftBase, 20, TRUE, FALSE, displayAls);
printPosOnChrom(seqName, rec->chromStart, rec->chromEnd, NULL, FALSE, rec->name);
printf("<B>Reference allele:</B> %s<BR>\n", displayAls[0]);
vcfAltAlleleDetails(rec, displayAls);
vcfQualDetails(rec);
vcfFilterDetails(rec);
vcfInfoDetails(rec);
pgSnpCodingDetail(rec);
makeDisplayAlleles(rec, showLeftBase, leftBase, 5, FALSE, TRUE, displayAls);
vcfGenotypesDetails(rec, tdb, displayAls);
}
static struct pgSnp *vcfFileToPgSnp(struct vcfFile *vcff, struct trackDb *tdb)
/* Convert vcff's records to pgSnp; don't free vcff until you're done with pgSnp
* because it contains pointers into vcff's records' chrom. */
{
struct pgSnp *pgsList = NULL;
struct vcfRecord *rec;
int maxLen = 33;
int maxAlCount = 5;
for (rec = vcff->records; rec != NULL; rec = rec->next)
{
struct pgSnpVcfStartEnd *psvs = needMem(sizeof(*psvs));
psvs->vcfStart = vcfRecordTrimIndelLeftBase(rec);
psvs->vcfEnd = vcfRecordTrimAllelesRight(rec);
struct pgSnp *pgs = pgSnpFromVcfRecord(rec);
memcpy(&(psvs->pgs), pgs, sizeof(*pgs));
pgs = (struct pgSnp *)psvs; // leak mem
// Insertion sequences can be quite long; abbreviate here for display.
int len = strlen(pgs->name);
if (len > maxLen)
{
int maxAlLen = (maxLen / min(rec->alleleCount, maxAlCount)) - 1;
pgs->name[0] = '\0';
int i;
for (i = 0; i < rec->alleleCount; i++)
{
if (i > 0)
safencat(pgs->name, len+1, "/", 1);
if (i >= maxAlCount)
{
safecat(pgs->name, len+1, "...");
pgs->alleleCount = maxAlCount;
break;
}
if (strlen(rec->alleles[i]) > maxAlLen-3)
strcpy(rec->alleles[i]+maxAlLen-3, "...");
safencat(pgs->name, len+1, rec->alleles[i], maxAlLen);
}
}
slAddHead(&pgsList, pgs);
}
slReverse(&pgsList);
return pgsList;
}
static void drawOneRec(struct vcfRecord *rec, unsigned short *gtHapOrder, unsigned short gtHapCount,
struct track *tg, struct hvGfx *hvg, int xOff, int yOff, int width,
boolean isClustered, boolean isCenter, enum hapColorMode colorMode)
/* Draw a stack of genotype bars for this record */
{
unsigned int chromStartMap = vcfRecordTrimIndelLeftBase(rec);
unsigned int chromEndMap = vcfRecordTrimAllelesRight(rec);
const double scale = scaleForPixels(width);
int x1 = round((double)(rec->chromStart-winStart)*scale) + xOff;
int x2 = round((double)(rec->chromEnd-winStart)*scale) + xOff;
int w = x2-x1;
if (w <= 1)
{
x1--;
w = 3;
}
// When coloring mode is altOnly, we draw one extra pixel row at the top & one at bottom
// to show the locations of variants, since the reference alleles are invisible:
int extraPixel = 0;
int hapHeight = tg->height - CLIP_PAD;
if (colorMode == altOnlyMode)
{
hvGfxLine(hvg, x1, yOff, x2, yOff, (isClustered ? purple : shadesOfGray[5]));
extraPixel = 1;
hapHeight -= extraPixel*2;
}
double hapsPerPix = (double)gtHapCount / hapHeight;
int pixIx;
for (pixIx = 0; pixIx < hapHeight; pixIx++)
{
int gtHapOrderIxStart = (int)(hapsPerPix * pixIx);
int gtHapOrderIxEnd = round(hapsPerPix * (pixIx + 1));
if (gtHapOrderIxEnd == gtHapOrderIxStart)
gtHapOrderIxEnd++;
int unks = 0, refs = 0, alts = 0;
int gtHapOrderIx;
for (gtHapOrderIx = gtHapOrderIxStart; gtHapOrderIx < gtHapOrderIxEnd; gtHapOrderIx++)
{
int gtHapIx = gtHapOrder[gtHapOrderIx];
int hapIx = gtHapIx & 1;
int gtIx = gtHapIx >>1;
struct vcfGenotype *gt = &(rec->genotypes[gtIx]);
if (gt->isPhased || gt->isHaploid || (gt->hapIxA == gt->hapIxB))
{
int alIx = hapIx ? gt->hapIxB : gt->hapIxA;
if (alIx < 0)
unks++;
else if (alIx > 0)
alts++;
else
refs++;
}
else
unks++;
}
int y = yOff + extraPixel + pixIx;
Color col;
if (colorMode == baseMode)
col = colorByBase(refs, alts, unks, rec->alleles[0], rec->alleles[1]);
else if (colorMode == refAltMode)
col = colorByRefAlt(refs, alts, unks);
else
col = colorByAltOnly(refs, alts, unks);
if (col != MG_WHITE)
hvGfxLine(hvg, x1, y, x2, y, col);
}
int yBot = yOff + tg->height - CLIP_PAD - 1;
if (isCenter)
{
if (colorMode == altOnlyMode)
{
// Colorful outline to distinguish this variant:
hvGfxLine(hvg, x1-1, yOff, x1-1, yBot, purple);
hvGfxLine(hvg, x2+1, yOff, x2+1, yBot, purple);
hvGfxLine(hvg, x1-1, yOff, x2+1, yOff, purple);
hvGfxLine(hvg, x1-1, yBot, x2+1, yBot, purple);
}
else
{
// Thick black lines to distinguish this variant:
hvGfxBox(hvg, x1-3, yOff, 3, tg->height, MG_BLACK);
hvGfxBox(hvg, x2, yOff, 3, tg->height, MG_BLACK);
hvGfxLine(hvg, x1-2, yOff, x2+2, yOff, MG_BLACK);
hvGfxLine(hvg, x1-2, yBot, x2+2, yBot, MG_BLACK);
}
// Mouseover was handled already by mapBoxForCenterVariant
}
else
{
struct dyString *dy = dyStringNew(0);
gtSummaryString(rec, dy);
mapBoxHgcOrHgGene(hvg, chromStartMap, chromEndMap, x1, yOff, w, tg->height, tg->track,
rec->name, dy->string, NULL, TRUE, NULL);
}
if (colorMode == altOnlyMode)
hvGfxLine(hvg, x1, yBot, x2, yBot, (isClustered ? purple : shadesOfGray[5]));
}
