9d1afd2a9f40d137353e53d7f1d0df4ca25fe4b7 max Wed Sep 4 16:04:11 2024 -0700 removing hubId from table browser fasta output, refs #34396 diff --git src/hg/cgilib/hgSeq.c src/hg/cgilib/hgSeq.c index 694ac16..f0b6f9a 100644 --- src/hg/cgilib/hgSeq.c +++ src/hg/cgilib/hgSeq.c @@ -5,30 +5,31 @@ #include "common.h" #include "hCommon.h" #include "dnautil.h" #include "dnaseq.h" #include "dystring.h" #include "cart.h" #include "cheapcgi.h" #include "hdb.h" #include "web.h" #include "rmskOut.h" #include "fa.h" #include "genePred.h" #include "bed.h" #include "hgSeq.h" #include "trackHub.h" +#include "hubConnect.h" int hgSeqChromSize(char *db, char *chromName) /* get chrom size if there's a database out there, * otherwise just return 0 */ { int thisSize = 0; if (hDbExists(db)) thisSize = hChromSize(db, chromName); return thisSize; } void hgSeqFeatureRegionOptions(struct cart *cart, boolean canDoUTR, boolean canDoIntrons) /* Print out HTML FORM entries for feature region options. */ @@ -432,32 +433,32 @@ if (isRc && !toPrimer3) reverseComplement(cSeq->dna, cSeq->size); if (toPrimer3) { struct dyString* primer3Exons = genPrimer3Exons(rCount, rStarts, rSizes, exonFlags, seqStart); printPrimerForm(cSeq->dna, primer3Exons->string, db, strand, hgAbsUrlCgi("hgTracks")); dyStringFree(&primer3Exons); } else { safef(recName, sizeof(recName), "%s_%s range=%s:%d-%d 5'pad=%d 3'pad=%d " "strand=%c repeatMasking=%s", - db, - name, + hubConnectSkipHubPrefix(db), + hubConnectSkipHubPrefix(name), chrom, seqStart+1, seqEnd, padding5, padding3, (isRc ? '-' : '+'), (maskRep ? repMasking : "none")); faWriteNext(stdout, recName, cSeq->dna, cSeq->size); freeDnaSeq(&cSeq); } } static void hgSeqRegionsAdjDb(char *db, char *chrom, int chromSize, char strand, char *name, boolean concatRegions, boolean concatAdjacent, int rCount, unsigned *rStarts, unsigned *rSizes, boolean *exonFlags, boolean *cdsFlags, boolean toPrimer3) /* Concatenate and print out dna for a series of regions,