e08ae97dc288749c2454fd98a10dc79f06e27cb5 max Tue Aug 11 06:16:20 2026 -0700 hgBlat/hgc: fixes from the v502 code review of the BLAT results pages, refs #37893 #4 blatOldTracks now falls back to "keep" (with a warning) on any value other than keep/hide/delete, instead of dropping into the destructive delete branch, so a typo in hg.conf can never silently discard a user's earlier BLAT tracks. #5 htmlEncode() (js/utils.js) now also escapes " and ', which the browser's text->markup conversion leaves alone. Every hgBlat caller puts the result in a double-quoted attribute, so an unescaped quote in the cart position string could break out of the attribute; the shared helper now honors its documented contract. #6 The non-BLAT alignment title no longer starts with a stray space. #7 open_memstream() is checked for NULL: on that failure the alignment renders straight to stdout instead of writing to a NULL FILE and calling fclose(NULL). The section reorder keys on the literal "<H4><A NAME=genomic>"/"<H4><A NAME=ali>" strings, so a note was added in fuzzyShow.c and pslShow.c to keep them intact. Found in the v502 final-build code review, refs #38069. diff --git src/lib/fuzzyShow.c src/lib/fuzzyShow.c index 59e385177db..d792f50917d 100644 --- src/lib/fuzzyShow.c +++ src/lib/fuzzyShow.c @@ -287,30 +287,32 @@ reverseComplement(needle, needleSize); if (showNeedle) { ffShNeedle(f, needle, needleSize, needleNumOffset, colorFlags, aliList, upcMatch, cdsS, cdsE, restrictToWindow, nPartS, nPartE); } if (showHaystack) { struct cfm *cfm = cfmNew(10, 50, TRUE, rcHaystack, f, hayExtremity); char *h = cloneMem(haystack, haySize); char *accentFlags = needMem(haySize); zeroBytes(accentFlags, haySize); + /* hgc's htcBlatAlignment reorders these sections by matching the literal "<H4><A NAME=genomic>" + * and "<H4><A NAME=ali>" prefixes; keep them intact (or update hgc.c) so the reorder still fires. */ fprintf(f, "<H4><A NAME=genomic></A>Genomic %s %s:</H4>\n", haystackName, (rcHaystack ? "(reverse strand)" : "")); fprintf(f, "<PRE><TT>\n"); zeroBytes(colorFlags, haySize); for (ali = leftAli; ali != NULL; ali = ali->right) { boolean utr = FALSE; int i; int off = ali->hStart-haystack; int count = ali->hEnd - ali->hStart; int offn = ali->nStart-needle; if ((cdsE > 0) && ((cdsS-offn-1) > 0)) utr = TRUE; for (i=0; i<count; ++i)