c4770655923d38c3c11c09c528b6b800b4785269
braney
  Mon Jul 11 09:45:53 2016 -0700
don't use htcGetDnaAliInWindow if you want to show alignments outside
the window

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index fd7259b..d1ef0f1 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -7258,31 +7258,31 @@
 if (sameString("mrnaBlastz", aliTable) || sameString("pseudoMrna", aliTable))
     {
     struct sqlConnection *conn = hAllocConn(database);
     unsigned retId = 0;
     safef(accTmp, sizeof accTmp, "bz-%s", acc);
     if (hRnaSeqAndIdx(accTmp, &rnaSeq, &retId, conn) == -1)
         rnaSeq = hRnaSeq(database, acc);
     hFreeConn(&conn);
     }
 else if (sameString("HInvGeneMrna", aliTable))
     {
     /* get RNA accession for the gene id in the alignment */
     sqlSafef(query, sizeof query, "select mrnaAcc from HInv where geneId='%s'", acc);
     rnaSeq = hRnaSeq(database, sqlQuickString(conn, query));
     }
-else if (sameString("ncbiRefSeqPsl", aliTable))
+else if (sameString("ncbiRefSeqPsl", aliTable) || startsWith("altSeqLiftOverPsl", aliTable))
     {
     rnaSeq = getBaseColorSequence(acc, aliTable);
     }
 else
     {
     char *cdnaTable = NULL;
     struct trackDb *tdb = hashFindVal(trackHash, aliTable);
     if (tdb != NULL)
 	cdnaTable = trackDbSetting(tdb, "cdnaTable");
     if (isNotEmpty(cdnaTable) && hTableExists(database, cdnaTable))
 	rnaSeq = hGenBankGetMrna(database, acc, cdnaTable);
     else
 	rnaSeq = hRnaSeq(database, acc);
     }
 
@@ -8692,31 +8692,31 @@
 int total = 0, i = 0;
 struct psl *pslList = NULL;
 struct sqlConnection *conn = hAllocConn(database);
 // char *otherDb = trackDbSetting(tdb, "otherDb");
 // int altSize = hChromSize(otherDb, item);
 
 genericHeader(tdb, item);
 printCustomUrl(tdb, item, TRUE);
 
 puts("<P>");
 puts("<B>Alignment Summary:</B><BR>\n");
 // char strBuf[64];
 // sprintLongWithCommas(strBuf, altSize);
 // printf("<B>Alignment Summary: '%s' %s</B><BR>\n", item, strBuf);
 pslList = getAlignments(conn, tdb->table, item);
-printAlignments(pslList, start, "htcCdnaAliInWindow", tdb->table, item);
+printAlignments(pslList, start, "htcCdnaAli", tdb->table, item);
 
 puts("<P>");
 total = 0;
 for (i=0;  i < pslList -> blockCount;  i++)
     {
     total += pslList->blockSizes[i];
     }
 printf("%d block(s) covering %d bases<BR>\n"
        "%d matching bases<BR>\n"
        "%d mismatching bases<BR>\n"
        "%d N bases<BR>\n"
        "%d bases inserted in %s<BR>\n"
        "%d bases inserted in %s<BR>\n"
        "score: %d<BR>\n",
        pslList->blockCount, total,