9c25510eb2cbb183c4e630d3519c693d33672dec angie Mon Jul 18 16:59:07 2016 -0700 dbSNP includes some deletions >1kbp so just clone the reference allele instead of trying to copy into finite-size char[]. However, abbreviate really long alleles for display so they don't mess up the page. refs #10937. diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c index 739c2c6..c1276d6 100644 --- src/hg/hgc/hgc.c +++ src/hg/hgc/hgc.c @@ -16999,64 +16999,76 @@ char **row; char query[512]; sqlSafef(query, sizeof(query), "select chimpAllele from %s where name='%s'", orthoTable, rsId); sr = sqlGetResult(conn, query); if ((row = sqlNextRow(sr)) != NULL) printf("<B>Summary: </B>%s>%s (chimp allele displayed first, " "then '>', then human alleles)<br>\n", row[0], observed); sqlFreeResult(&sr); hFreeConn(&conn); } } #define FOURBLANKCELLS "<TD></TD><TD></TD><TD></TD><TD></TD>" +static char *abbreviateAllele(char *allele) +/* If allele is >50bp then return an abbreviated version with first & last 20 bases and length; + * otherwise just return (cloned) allele. */ +{ +int length = strlen(allele); +if (length > 50) + { + struct dyString *dyAbbr = dyStringCreate("%.20s", allele); + dyStringAppend(dyAbbr, "..."); + dyStringAppend(dyAbbr, allele+length - 20); + dyStringPrintf(dyAbbr, " (%d bases)", length); + return dyStringCannibalize(&dyAbbr); + } +return cloneString(allele); +} + void printSnpAlleleRows(struct snp125 *snp, int version) /* Print the UCSC ref allele (and dbSNP if it differs), as row(s) of a * 6-column table. */ { if (sameString(snp->strand,"+") || strchr(snp->refUCSC, '(')) // don't try to revComp refUCSC if it is "(N bp insertion)" etc. { printf("<TR><TD><B>Reference allele: </B></TD>" - "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", snp->refUCSC); + "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", abbreviateAllele(snp->refUCSC)); if (!sameString(snp->refUCSC, snp->refNCBI)) printf("<TR><TD><B>dbSnp reference allele: </B></TD>" - "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", snp->refNCBI); + "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", abbreviateAllele(snp->refNCBI)); } else if (sameString(snp->strand,"-")) { - char refUCSCRevComp[1024]; - if (sameString(snp->strand, "-")) - { - safef(refUCSCRevComp, sizeof(refUCSCRevComp), "%s", snp->refUCSC); + char *refUCSCRevComp = cloneString(snp->refUCSC); reverseComplement(refUCSCRevComp, strlen(refUCSCRevComp)); - } printf("<TR><TD><B>Reference allele: </B></TD>" - "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", refUCSCRevComp); + "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", abbreviateAllele(refUCSCRevComp)); if (version < 127 && !sameString(refUCSCRevComp, snp->refNCBI)) printf("<TR><TD><B>dbSnp reference allele: </B></TD>" - "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", snp->refNCBI); + "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", abbreviateAllele(snp->refNCBI)); else if (version >= 127 && !sameString(snp->refUCSC, snp->refNCBI)) { - char refNCBIRevComp[1024]; - safecpy(refNCBIRevComp, sizeof(refNCBIRevComp), snp->refNCBI); + char *refNCBIRevComp = cloneString(snp->refNCBI); + if (! strchr(snp->refNCBI, '(')) reverseComplement(refNCBIRevComp, strlen(refNCBIRevComp)); printf("<TR><TD><B>dbSnp reference allele: </B></TD>" "<TD align=center>%s</TD>"FOURBLANKCELLS"</TR>\n", - refNCBIRevComp); + abbreviateAllele(refNCBIRevComp)); } } } #define TINYPADDING 3 void printSnpOrthoOneRow(char *orthoName, char *orthoDb, char *orthoAllele, char *orthoStrand, char *orthoChrom, int orthoStart, int orthoEnd) /* Print out a 6-column table row describing an orthologous allele. */ { printf("<TR><TD><B>%s allele: </B></TD>" "<TD align=center>%s</TD>\n", orthoName, orthoAllele); if (!sameString(orthoAllele, "?")) { printf("<TD> <B>%s strand: </B></TD>" @@ -17296,44 +17308,42 @@ else if (offset == 0) dyStringPrintf(dy, "<B>%c</B>%c%c", codon[0], codon[1], codon[2]); else if (offset == 1) dyStringPrintf(dy, "%c<B>%c</B>%c", codon[0], codon[1], codon[2]); else if (offset == 2) dyStringPrintf(dy, "%c%c<B>%c</B>", codon[0], codon[1], codon[2]); else dyStringAppend(dy, codon); return dy->string; } void printSnp125FunctionInCDS(struct snp125 *snp, char *geneTable, char *geneTrack, struct genePred *gene, int exonIx, char *geneName) /* Show the effect of each observed allele of snp on the given exon of gene. */ { -char refAllele[1024]; -safecpy(refAllele, sizeof(refAllele), snp->refUCSC); +char *refAllele = cloneString(snp->refUCSC); boolean refIsAlpha = isalpha(refAllele[0]); boolean geneIsRc = sameString(gene->strand, "-"), snpIsRc = sameString(snp->strand, "-"); if (geneIsRc && refIsAlpha) reverseComplement(refAllele, strlen(refAllele)); int refAlleleSize = sameString(refAllele, "-") ? 0 : refIsAlpha ? strlen(refAllele) : -1; boolean refIsSingleBase = (refAlleleSize == 1 && refIsAlpha); int snpCodonPos = 0; char refCodon[4], refAA = '\0'; if (refIsSingleBase) getSnp125RefCodonAndSnpPos(snp, gene, exonIx, &snpCodonPos, refCodon, &refAA); -char alleleStr[1024]; -safecpy(alleleStr, sizeof(alleleStr), snp->observed); +char *alleleStr = cloneString(snp->observed); char *indivAlleles[64]; int alleleCount = chopString(alleleStr, "/", indivAlleles, ArraySize(indivAlleles)); int j; for (j = 0; j < alleleCount; j++) { char *al = indivAlleles[j]; boolean alIsAlpha = (isalpha(al[0]) && !sameString(al, "lengthTooLong")); if ((snpIsRc ^ geneIsRc) && alIsAlpha) reverseComplement(al, strlen(al)); char alBase = al[0]; if (alBase == '\0' || sameString(al, refAllele)) continue; int alSize = sameString(al, "-") ? 0 : alIsAlpha ? strlen(al) : -1; if (alSize != refAlleleSize && alSize >= 0 && refAlleleSize >=0) { @@ -17378,31 +17388,32 @@ } else { if (refAA == '*') printf(firstTwoColumnsPctS "%s %c (%s) --> %c (%s)\n", geneTrack, geneName, snpMisoLinkFromFunc("stop_retained_variant"), refAA, refCodonHtml, snpAA, snpCodonHtml); else printf(firstTwoColumnsPctS "%s %c (%s) --> %c (%s)\n", geneTrack, geneName, snpMisoLinkFromFunc("coding-synon"), refAA, refCodonHtml, snpAA, snpCodonHtml); } } else printf(firstTwoColumnsPctS "%s %s --> %s\n", - geneTrack, geneName, snpMisoLinkFromFunc("cds-synonymy-unknown"), refAllele, al); + geneTrack, geneName, snpMisoLinkFromFunc("cds-synonymy-unknown"), + abbreviateAllele(refAllele), abbreviateAllele(al)); } } void printSnp125FunctionInGene(struct snp125 *snp, char *geneTable, char *geneTrack, struct genePred *gene) /* Given a SNP and a gene that overlaps it, say where in the gene it overlaps * and if in CDS, say what effect the coding alleles have. */ { int snpStart = snp->chromStart, snpEnd = snp->chromEnd; int cdsStart = gene->cdsStart, cdsEnd = gene->cdsEnd; boolean geneIsRc = sameString(gene->strand, "-"); char *geneName = getSymbolForGeneName(geneTable, gene->name); int i, iStart = 0, iEnd = gene->exonCount, iIncr = 1; if (geneIsRc) { iStart = gene->exonCount - 1; iEnd = -1; iIncr = -1; }