c20579fc7c537c1736650125c5d264357d2cfa78 angie Mon Sep 18 13:15:16 2017 -0700 Big search & replace: use https instead of http for NCBI URLs. refs #17793 diff --git src/hg/hgc/vcfClick.c src/hg/hgc/vcfClick.c index 496f5c2..80ce88f 100644 --- src/hg/hgc/vcfClick.c +++ src/hg/hgc/vcfClick.c @@ -1,601 +1,601 @@ /* vcfTrack -- handlers for Variant Call Format data. */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "dystring.h" #include "errCatch.h" #include "hCommon.h" #include "hdb.h" #include "hgc.h" #include "htmshell.h" #include "jsHelper.h" #include "pgSnp.h" #include "regexHelper.h" #include "trashDir.h" #include "knetUdc.h" #include "udc.h" #include "vcf.h" #include "vcfUi.h" #define NA "<em>n/a</em>" static void printKeysWithDescriptions(struct vcfFile *vcff, int wordCount, char **words, struct vcfInfoDef *infoDefs, boolean stripToSymbol) /* Given an array of keys, print out a list of values with descriptions if descriptions are * available. If stripToSymbol, when searching infoDefs, pick the actual key out of * <>'s and other extraneous stuff (e.g. "(C)<DEL>" --> "DEL"). */ { int i; for (i = 0; i < wordCount; i++) { if (i > 0) printf(", "); char *displayKey = words[i]; char *descKey = displayKey; if (stripToSymbol) { char *p = strchr(displayKey, '<'); if (p) { descKey = cloneString(p+1); p = strchr(descKey, '>'); if (p) *p = '\0'; } } char *description = NULL; struct vcfInfoDef *def; for (def = infoDefs; def != NULL; def = def->next) if (sameString(descKey, def->key)) { description = def->description; break; } char *htmlKey = htmlEncode(displayKey); if (description) printf("%s (%s)", htmlKey, description); else printf("%s", htmlKey); } printf("<BR>\n"); } static void vcfAltAlleleDetails(struct vcfRecord *rec, char **displayAls) /* If VCF header specifies any symbolic alternate alleles, pull in descriptions. */ { printf("<B>Alternate allele(s):</B> "); if (rec->alleleCount < 2 || sameString(rec->alleles[1], ".")) { printf(NA"<BR>\n"); return; } struct vcfFile *vcff = rec->file; printKeysWithDescriptions(vcff, rec->alleleCount-1, &(displayAls[1]), vcff->altDefs, TRUE); } static void vcfQualDetails(struct vcfRecord *rec) /* If VCF header specifies a quality/confidence score (not "."), print it out. */ { printf("<B>Quality/confidence score:</B> %s<BR>\n", sameString(rec->qual, ".") ? NA : rec->qual); } static void vcfFilterDetails(struct vcfRecord *rec) /* If VCF header specifies any filters, pull in descriptions. */ { if (rec->filterCount == 0 || sameString(rec->filters[0], ".")) printf("<B>Filter:</B> "NA"<BR>\n"); else if (rec->filterCount == 1 && sameString(rec->filters[0], "PASS")) printf("<B>Filter:</B> PASS<BR>\n"); else { printf("<B>Filter failures:</B> "); printf("<font style='font-weight: bold; color: #FF0000;'>\n"); struct vcfFile *vcff = rec->file; printKeysWithDescriptions(vcff, rec->filterCount, rec->filters, vcff->filterDefs, FALSE); printf("</font>\n"); } } // Characters we expect to see in |-separated parts of an ##INFO description that specifies // tabular contents: #define COL_DESC_WORD_REGEX "[A-Za-z_0-9.-]+" // Series of |-separated words: #define COL_DESC_REGEX COL_DESC_WORD_REGEX"(\\|"COL_DESC_WORD_REGEX")+" // Minimum number of |-separated values for interpreting descriptions and values as tabular: #define MIN_COLUMN_COUNT 3 static boolean looksTabular(const struct vcfInfoDef *def, struct vcfInfoElement *el) /* Return TRUE if def->description seems to contain a |-separated description of columns * and el's first non-empty string value has the same number of |-separated parts. */ { if (!def || def->type != vcfInfoString || isEmpty(def->description)) return FALSE; if (regexMatch(def->description, COL_DESC_REGEX)) { int descColCount = countChars(def->description, '|') + 1; if (descColCount >= MIN_COLUMN_COUNT) { int j; for (j = 0; j < el->count; j++) { char *val = el->values[j].datString; if (isEmpty(val)) continue; int elColCount = countChars(val, '|') + 1; if (elColCount == descColCount) return TRUE; } } } return FALSE; } static void printTabularHeaderRow(const struct vcfInfoDef *def) /* Parse the column header parts out of def->description and print as table header row; * call this only when looksTabular returns TRUE. */ { regmatch_t substrArr[PATH_LEN]; if (regexMatchSubstr(def->description, COL_DESC_REGEX, substrArr, ArraySize(substrArr))) { puts("<TR>"); // Make a copy of the part of def->description that matches the regex, // then chop by '|' and print out header column tags: int matchSize = substrArr[0].rm_eo - substrArr[0].rm_so; char copy[matchSize+1]; safencpy(copy, sizeof(copy), def->description + substrArr[0].rm_so, matchSize); // Turn '_' into ' ' so description words can wrap inside headers, saving some space subChar(copy, '_', ' '); char *words[PATH_LEN]; int descColCount = chopByChar(copy, '|', words, ArraySize(words)); int i; for (i = 0; i < descColCount; i++) printf("<TH class='withThinBorder'>%s</TH>", words[i]); puts("</TR>"); } else errAbort("printTabularHeaderRow: code bug, if looksTabular returns true then " "regex should work here"); } static void printTabularData(struct vcfInfoElement *el) /* Print a row for each value in el, separating columns by '|'. */ { int j; for (j = 0; j < el->count; j++) { puts("<TR>"); char *val = el->values[j].datString; if (!isEmpty(val)) { int len = strlen(val); char copy[len+1]; safencpy(copy, sizeof(copy), val, len); char *words[PATH_LEN]; int colCount = chopByChar(copy, '|', words, ArraySize(words)); int k; for (k = 0; k < colCount; k++) printf("<TD class='withThinBorder'>%s</TD>", words[k]); } puts("</TR>"); } } static void vcfInfoDetails(struct vcfRecord *rec) /* Expand info keys to descriptions, then print out keys and values. */ { if (rec->infoCount == 0) return; struct vcfFile *vcff = rec->file; puts("<B>INFO column annotations:</B><BR>"); puts("<TABLE border=0 cellspacing=0 cellpadding=2>"); int i; for (i = 0; i < rec->infoCount; i++) { struct vcfInfoElement *el = &(rec->infoElements[i]); const struct vcfInfoDef *def = vcfInfoDefForKey(vcff, el->key); printf("<TR valign='top'><TD align=\"right\"><B>%s:</B></TD><TD>", el->key); int j; enum vcfInfoType type = def ? def->type : vcfInfoString; if (type == vcfInfoFlag && el->count == 0) printf("Yes"); // no values, so we can't call vcfPrintDatum... // However, if this is older VCF, type vcfInfoFlag might have a value. if (looksTabular(def, el)) { // Make a special display below printf("<em>see below</em>"); } else { for (j = 0; j < el->count; j++) { if (j > 0) printf(", "); if (el->missingData[j]) printf("."); else vcfPrintDatum(stdout, el->values[j], type); } } if (def != NULL) printf(" </TD><TD>%s", def->description); else printf("</TD><TD>"); printf("</TD></TR>\n"); } puts("</TABLE>"); // Now show the tabular fields, if any for (i = 0; i < rec->infoCount; i++) { struct vcfInfoElement *el = &(rec->infoElements[i]); const struct vcfInfoDef *def = vcfInfoDefForKey(vcff, el->key); if (looksTabular(def, el)) { puts("<BR>"); printf("<B>%s</B>: %s<BR>\n", el->key, def->description); puts("<TABLE class='stdTbl'>"); printTabularHeaderRow(def); printTabularData(el); puts("</TABLE>"); } } } static void vcfGenotypeTable(struct vcfRecord *rec, char *track, char **displayAls) /* Put the table containing details about each genotype into a collapsible section. */ { static struct dyString *tmp1 = NULL; if (tmp1 == NULL) tmp1 = dyStringNew(0); jsBeginCollapsibleSection(cart, track, "genotypes", "Detailed genotypes", FALSE); dyStringClear(tmp1); dyStringAppend(tmp1, rec->format); struct vcfFile *vcff = rec->file; enum vcfInfoType formatTypes[256]; char *formatKeys[256]; int formatCount = chopString(tmp1->string, ":", formatKeys, ArraySize(formatKeys)); puts("<B>Genotype info key:</B><BR>"); int i; for (i = 0; i < formatCount; i++) { if (sameString(formatKeys[i], vcfGtGenotype)) continue; const struct vcfInfoDef *def = vcfInfoDefForGtKey(vcff, formatKeys[i]); char *desc = def ? def->description : "<em>not described in VCF header</em>"; printf(" <B>%s:</B> %s<BR>\n", formatKeys[i], desc); formatTypes[i] = def->type; } hTableStart(); puts("<TR><TH>Sample ID</TH><TH>Genotype</TH><TH>Phased?</TH>"); for (i = 0; i < formatCount; i++) { if (sameString(formatKeys[i], vcfGtGenotype)) continue; printf("<TH>%s</TH>", formatKeys[i]); } puts("</TR>\n"); for (i = 0; i < vcff->genotypeCount; i++) { struct vcfGenotype *gt = &(rec->genotypes[i]); char *hapA = ".", *hapB = "."; if (gt->hapIxA >= 0) hapA = displayAls[(unsigned char)gt->hapIxA]; if (gt->isHaploid) hapB = ""; else if (gt->hapIxB >= 0) hapB = displayAls[(unsigned char)gt->hapIxB]; char sep = gt->isHaploid ? ' ' : gt->isPhased ? '|' : '/'; char *phasing = gt->isHaploid ? NA : gt->isPhased ? "Y" : "n"; printf("<TR><TD>%s</TD><TD>%s%c%s</TD><TD>%s</TD>", vcff->genotypeIds[i], hapA, sep, hapB, phasing); int j; for (j = 0; j < gt->infoCount; j++) { if (sameString(formatKeys[j], vcfGtGenotype)) continue; printf("<TD>"); struct vcfInfoElement *el = &(gt->infoElements[j]); int k; for (k = 0; k < el->count; k++) { if (k > 0) printf(", "); if (el->missingData[k]) printf("."); else vcfPrintDatum(stdout, el->values[k], formatTypes[j]); } printf("</TD>"); } puts("</TR>"); } hTableEnd(); jsEndCollapsibleSection(); } static void ignoreEm(char *format, va_list args) /* Ignore warnings from genotype parsing -- when there's one, there * are usually hundreds more just like it. */ { } 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 pgSnpCodingDetail(struct vcfRecord *rec) /* Translate rec into pgSnp (with proper chrom name) and call Belinda's * coding effect predictor from pgSnp details. */ { char *genePredTable = "knownGene"; if (hTableExists(database, genePredTable)) { struct pgSnp *pgs = pgSnpFromVcfRecord(rec); if (!sameString(rec->chrom, seqName)) // rec->chrom might be missing "chr" prefix: pgs->chrom = seqName; printSeqCodDisplay(database, pgs, genePredTable); } } static void abbreviateLongSeq(char *seqIn, int endLength, boolean showLength, struct dyString *dy) /* If seqIn is longer than 2*endLength plus abbreviation fudge, abbreviate it * to its first endLength bases, ellipsis that says how many bases are skipped, * and its last endLength bases; add result to dy. */ { int threshold = 2*endLength + 30; int seqInLen = strlen(seqIn); if (seqInLen > threshold) { dyStringAppendN(dy, seqIn, endLength); dyStringAppend(dy, "..."); if (showLength) { int skippedLen = seqInLen-2*endLength; dyStringPrintf(dy, "<%d bases>...", skippedLen); } dyStringAppend(dy, seqIn+seqInLen-endLength); } else dyStringAppend(dy, seqIn); } static void makeDisplayAlleles(struct vcfRecord *rec, boolean showLeftBase, char leftBase, int endLength, boolean showLength, boolean encodeHtml, char **displayAls) /* If necessary, show the left base that we trimmed and/or abbreviate long sequences. */ { struct dyString *dy = dyStringNew(128); int i; for (i = 0; i < rec->alleleCount; i++) { dyStringClear(dy); if (showLeftBase) dyStringPrintf(dy, "(%c)", leftBase); abbreviateLongSeq(rec->alleles[i], endLength, showLength, dy); if (encodeHtml) displayAls[i] = htmlEncode(dy->string); else displayAls[i] = cloneString(dy->string); } } 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"). */ { if (isNotEmpty(rec->name) && differentString(rec->name, ".")) printf("<B>Name:</B> %s<BR>\n", rec->name); if (sameString(tdb->track, "exacVariants")) { printf("<b>ExAC:</b> " "<a href=\"http://exac.broadinstitute.org/variant/%s-%d-%s-%s\" " "target=_blank>%s:%d %s/%s</a><br>\n", skipChr(rec->chrom), rec->chromStart+1, rec->alleles[0], rec->alleles[1], skipChr(rec->chrom), rec->chromStart+1, rec->alleles[0], rec->alleles[1]); } // 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/\" " + printf("<A HREF=\"https://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); } void doVcfDetailsCore(struct trackDb *tdb, char *fileOrUrl, boolean isTabix) /* Show item details using fileOrUrl. */ { genericHeader(tdb, NULL); int start = cartInt(cart, "o"); int end = cartInt(cart, "t"); int vcfMaxErr = -1; struct vcfFile *vcff = NULL; /* protect against temporary network or parsing error */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { if (isTabix) { char *indexUrl = trackDbSetting(tdb, "bigDataIndex"); vcff = vcfTabixFileAndIndexMayOpen(fileOrUrl, indexUrl, seqName, start, end, vcfMaxErr, -1); } else vcff = vcfFileMayOpen(fileOrUrl, seqName, start, end, vcfMaxErr, -1, TRUE); } errCatchEnd(errCatch); if (errCatch->gotError) { if (isNotEmpty(errCatch->message->string)) warn("%s", errCatch->message->string); } errCatchFree(&errCatch); if (vcff != NULL) { struct vcfRecord *rec; for (rec = vcff->records; rec != NULL; rec = rec->next) if (rec->chromStart == start && rec->chromEnd == end) // in pgSnp mode, don't get name vcfRecordDetails(tdb, rec); } else printf("Sorry, unable to open %s<BR>\n", fileOrUrl); printTrackHtml(tdb); } void doVcfTabixDetails(struct trackDb *tdb, char *item) /* Show details of an alignment from a VCF file compressed and indexed by tabix. */ { knetUdcInstall(); if (udcCacheTimeout() < 300) udcSetCacheTimeout(300); struct sqlConnection *conn = hAllocConnTrack(database, tdb); char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, tdb->table, seqName); hFreeConn(&conn); doVcfDetailsCore(tdb, fileOrUrl, TRUE); } void doVcfDetails(struct trackDb *tdb, char *item) /* Show details of an alignment from an uncompressed VCF file. */ { struct customTrack *ct = lookupCt(tdb->track); struct sqlConnection *conn = NULL; char *table = tdb->table; if (ct) { conn = hAllocConn(CUSTOM_TRASH); table = ct->dbTableName; } else conn = hAllocConnTrack(database, tdb); char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, table, seqName); hFreeConn(&conn); doVcfDetailsCore(tdb, fileOrUrl, FALSE); }