5add048a3ba033e17e6c0f5643e9985ef8a15f44
max
  Thu Jun 13 02:59:16 2024 -0700
adding legend under cigar display on bam hgc page, refs #33292

diff --git src/hg/hgc/bamClick.c src/hg/hgc/bamClick.c
index 2d3c9b8..f80a35f 100644
--- src/hg/hgc/bamClick.c
+++ src/hg/hgc/bamClick.c
@@ -72,71 +72,77 @@
 /* Print out the properties of this alignment. */
 {
 const bam1_core_t *core = &bam->core;
 char *itemName = bam1_qname(bam);
 int tLength = bamGetTargetLength(bam);
 int tStart = core->pos, tEnd = tStart+tLength;
 boolean isRc = useStrand && bamIsRc(bam);
 printPosOnChrom(seqName, tStart, tEnd, NULL, FALSE, itemName);
 if (!skipQualityScore)
     printf("<B>Alignment Quality: </B>%d<BR>\n", core->qual);
 if (core->n_cigar > 50)
     printf("<B>CIGAR string: </B> Cannot show long CIGAR string, more than 50 operations. Contact us if you need to see the full CIGAR string here.<BR>\n");
 else
     {
     printf("<B>CIGAR string: </B><tt>%s</tt>", bamGetCigar(bam));
-    //bamShowCigarEnglish(bam);
     printf("<BR>\n");
+    //bamShowCigarEnglish(bam);
+    printf("<p><B>CIGAR Legend:</B><BR>"
+            "<b>M</b> : alignment match (seq. match or mismatch), <b>I</b> : insert from genome, <b>D</b> : deletion from genome, "
+            "<b>N</b> : skipped from genome, <BR>"
+            "<b>S</b> : soft clipping, <b>H</b> : hard clipping, <b>P</b> : padding, "
+            "<b>=</b> : sequence match, <b>X</b> : sequence mismatch\n");
+    printf("</p>\n");
     }
 
 int clippedBases[4];
 getClippedBases(bam, clippedBases);
 printf("<B>Start clipping:</B> hard: %d  soft: %d</BR>\n", clippedBases[0], clippedBases[1]);
 printf("<B>End clipping:</B> hard: %d  soft: %d</BR> \n", clippedBases[3], clippedBases[2]);
 
 printf("<B>Tags:</B>");
 bamShowTags(bam);
 puts("<BR>");
 printf("<B>Flags: </B><tt>0x%02x:</tt><BR>\n &nbsp;&nbsp;", core->flag);
 bamShowFlagsEnglish(bam);
 puts("<BR>");
 if (bamIsRc(bam))
     printf("<em>Note: although the read was mapped to the reverse strand of the genome, "
 	   "the sequence and CIGAR in BAM are relative to the forward strand.</em><BR>\n");
 puts("<BR>");
 struct dnaSeq *genoSeq = hChromSeq(database, seqName, tStart, tEnd);
 char *qSeq = bamGetQuerySequence(bam, FALSE);
 if (core->l_qseq > 5000)
-    printf("<B>Alignment not shown, very long sequence</B><BR>\n");
+    printf("<B>Alignment not shown, query sequence is %d bp long &gt; 5000bp</B><BR>\n", core->l_qseq);
 else
     {
     if (isNotEmpty(qSeq) && !sameString(qSeq, "*"))
         {
         char *qSeq = NULL;
         struct ffAli *ffa = bamToFfAli(bam, genoSeq, tStart, useStrand, &qSeq);
         printf("<B>Alignment of %s to %s:%d-%d%s:</B><BR>\n", itemName,
                seqName, tStart+1, tEnd, (isRc ? " (reverse complemented)" : ""));
         ffShowSideBySide(stdout, ffa, qSeq, 0, genoSeq->dna, tStart, tLength, 0, tLength, 8, isRc,
                          FALSE);
         }
     }
 
 if (!skipQualityScore && core->l_qseq > 0)
     {
     if (core->l_qseq > 5000)
         {
-        printf("<B>Sequence too long to show quality scores</B><BR>\n");
+        printf("<B>Sequence quality not shown, query sequence %d bp long &gt; 5000bp</B><BR>\n", core->l_qseq);
         } 
     else
         {
         printf("<B>Sequence quality scores:</B><BR>\n<TT><TABLE><TR>\n");
         UBYTE *quals = bamGetQueryQuals(bam, useStrand);
         int i;
         for (i = 0;  i < core->l_qseq;  i++)
             {
             if (i > 0 && (i % 24) == 0)
                 printf("</TR>\n<TR>");
             printf("<TD>%c<BR>%d</TD>", qSeq[i], quals[i]);
             }
         printf("</TR></TABLE></TT>\n");
         }
     }