d34fa1661ec45179035b50dc6ed47d8ea04835ac
lrnassar
  Thu Aug 1 13:28:48 2024 -0700
Tweaking the hgBlat warning message that was added recently to flow better, no RM.

diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c
index 4c0c80a..ebbbe84 100644
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@ -1699,36 +1699,38 @@
 
     if (++seqCount > maxSeqCount)
         {
 	warn("More than %d input sequences, stopping at %s<br>(see also: cgi-bin/hg.conf hgBlat.maxSequenceCount setting).",
 	    maxSeqCount, seq->name);
 	break;
 	}
     if (oneSize > maxSingleSize)
 	{
 	warn("Sequence %s is %d letters long (max is %d), skipping",
 	    seq->name, oneSize, maxSingleSize);
 	continue;
 	}
     if (oneSize < minSuggested)
         {
-	warn("Warning: Sequence %s is only %d letters long (%d is the recommended minimum).<br>"
-                "To search for short sequences in the current browser window, use our <a href='hgTrackUi?%s=%s&g=oligoMatch&oligoMatch=pack'>Short Sequence Match</a> track, "
-                "or, if you are using the command line and want to search the entire genome, our command line tool <tt>findMotifs</tt>, from the "
-                "<a target=_blank href='https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads'>utilities download page</a>.<br>"
-                "For primers, you can use our tool <a href='hgPcr?%s=%s'>In-silico PCR</a>. In-silico PCR searches the entire genome or a set of transcripts. In the latter case, it can find matches that straddle exon/intron boundaries.<br><br>"
-                "Contact us if none of these options solve the problem: genome@soe.ucsc.edu",
+	warn("Warning: Sequence %s is only %d letters long (%d is the recommended minimum).<br><br>"
+                "To search for short sequences in the browser window, use the <a href='hgTrackUi?%s=%s&g=oligoMatch&oligoMatch=pack'>Short Sequence Match</a> track. "
+                "You can also use our commandline tool <tt>findMotifs</tt> "
+                "(see <a target=_blank href='https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads'>utilities download page</a>) to "
+                "search for sequences on the entire genome.<br><br>"
+                "For primers, you can use the <a href='hgPcr?%s=%s'>In-silico PCR</a> tool. In-silico PCR can search the entire genome or a set of "
+                "transcripts. In the latter case, it can find matches that straddle exon/intron boundaries.<br><br>"
+                "Contact us for additional help using BLAT or its related tools: genome@soe.ucsc.edu",
 		seq->name, oneSize, minSuggested, cartSessionVarName(), cartSessionId(cart), cartSessionVarName(), cartSessionId(cart));
 	// we could use "continue;" here to actually enforce skipping, 
 	// but let's give the short sequence a chance, it might work.
 	// minimum possible length = tileSize+stepSize, so mpl=16 for dna stepSize=5, mpl=10 for protein.
 	if (qIsProt && oneSize < 1) // protein does not tolerate oneSize==0
 	    continue;
 	}
     totalSize += oneSize;
     if (totalSize > maxTotalSize)
         {
 	warn("Sequence %s would take us over the %d letter limit, stopping here.",
 	     seq->name, maxTotalSize);
 	break;
 	}