src/hg/hgc/bamClick.c 1.5

Index: src/hg/hgc/bamClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/bamClick.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/hgc/bamClick.c	21 Aug 2009 18:43:50 -0000	1.4
+++ src/hg/hgc/bamClick.c	21 Aug 2009 22:54:39 -0000	1.5
@@ -1,106 +1,148 @@
 /* bamClick - handler for alignments in BAM format (produced by MAQ,
  * BWA and some other short-read alignment tools). */
 #ifdef USE_BAM
 
 #include "common.h"
 #include "hash.h"
 #include "hdb.h"
 #include "bamFile.h"
 #include "hgc.h"
 
 static char const rcsid[] = "$Id$";
 
 #include "bamFile.h"
 
 struct bamTrackData
     {
     int itemStart;
     char *itemName;
     struct hash *pairHash;
     };
 
 static void singleBamDetails(const bam1_t *bam)
 /* 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 = ((core->flag & BAM_FREVERSE) != 0);
 printPosOnChrom(seqName, tStart, tEnd, (isRc ? "-" : "+"), FALSE, itemName);
 printf("<B>Flags: </B><tt>0x%02x</tt><BR>\n", core->flag);
 printf("<B>Alignment Quality: </B>%d<BR>\n", core->qual);
 printf("<B>CIGAR string: </B><tt>%s</tt><BR>\n", bamGetCigar(bam));
 char nibName[HDB_MAX_PATH_STRING];
 hNibForChrom(database, seqName, nibName);
 struct dnaSeq *genoSeq = hFetchSeq(nibName, seqName, tStart, tEnd);
 struct ffAli *ffa = bamToFfAli(bam, genoSeq, tStart);
 char *qSeq = ffa->nStart;
 printf("<BR><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);
+printf("<B>Tags:</B><BR>\n");
+
+// ugly: lifted from bam.c bam_format1:
+uint8_t *s = bam1_aux(bam);
+while (s < bam->data + bam->data_len)
+    {
+    uint8_t type, key[2];
+    key[0] = s[0]; key[1] = s[1];
+    s += 2; type = *s; ++s;
+    printf("\t%c%c:", key[0], key[1]);
+    if (type == 'A') { printf("A:%c", *s); ++s; }
+    else if (type == 'C') { printf("i:%u", *s); ++s; }
+    else if (type == 'c') { printf("i:%d", *s); ++s; }
+    else if (type == 'S') { printf("i:%u", *(uint16_t*)s); s += 2; }
+    else if (type == 's') { printf("i:%d", *(int16_t*)s); s += 2; }
+    else if (type == 'I') { printf("i:%u", *(uint32_t*)s); s += 4; }
+    else if (type == 'i') { printf("i:%d", *(int32_t*)s); s += 4; }
+    else if (type == 'f') { printf("f:%g", *(float*)s); s += 4; }
+    else if (type == 'd') { printf("d:%lg", *(double*)s); s += 8; }
+    else if (type == 'Z' || type == 'H')
+	{
+	printf("%c:", (char)type); 
+	while (*s) putc(*s++, stdout);
+	++s;
+	}
+    }
 //TODO: show flags properly, show tags, maybe display quality scores
 }
 
+static void bamPairDetails(const bam1_t *leftBam, const bam1_t *rightBam)
+/* Print out details for paired-end reads. */
+{
+printf("<TABLE><TR><TD><H4>Left end read</H4>\n");
+singleBamDetails(leftBam);
+printf("</TD><TD><H4>Right end read</H4>\n");
+singleBamDetails(rightBam);
+printf("</TD></TR></TABLE>\n");
+}
+
 static int oneBam(const bam1_t *bam, void *data)
 /* This is called on each record retrieved from a .bam file. */
 {
 const bam1_core_t *core = &bam->core;
 if (core->flag & BAM_FUNMAP)
     return 0;
 struct bamTrackData *btd = (struct bamTrackData *)data;
 if (sameString(bam1_qname(bam), btd->itemName))
     {
     if (btd->pairHash == NULL || (core->flag & BAM_FPAIRED) == 0)
 	{
 	if (core->pos == btd->itemStart)
 	    singleBamDetails(bam);
 	}
     else
 	{
-// TODO: paired: if this is first of pair, stash; if second, print details
-uglyf("<B>Note: </B>just showing half of a pair.<BR>\n");
-singleBamDetails(bam); // just for now.
+	bam1_t *firstBam = (bam1_t *)hashFindVal(btd->pairHash, btd->itemName);
+	if (firstBam == NULL)
+	    hashAdd(btd->pairHash, btd->itemName, bamClone(bam));
+	else
+	    {
+	    bamPairDetails(firstBam, bam);
+	    hashRemove(btd->pairHash, btd->itemName);
+	    }
 	}
     }
 return 0;
 }
 
 void doBamDetails(struct trackDb *tdb, char *item)
 /* Show details of an alignment from a BAM file. */
 {
 int start = cartInt(cart, "o");
 // make data structure and callback for pairing if necessary and printing out info
 // when we find our alignment.  If it has a stub, better search for the stub...
-//show position, sequence, quality, flags
 
 // TODO: libify
 char varName[1024];
 safef(varName, sizeof(varName), "%s_pairEndsByName", tdb->tableName);
 boolean isPaired = cartUsualBoolean(cart, varName,
 				    (trackDbSetting(tdb, "pairEndsByName") != NULL));
 
 // TODO: libify
 char *seqNameForBam = seqName;
 char *stripPrefix = trackDbSetting(tdb, "stripPrefix");
 if (stripPrefix && startsWith(stripPrefix, seqName))
     seqNameForBam = seqName + strlen(stripPrefix);
 char posForBam[512];
 safef(posForBam, sizeof(posForBam), "%s:%d-%d", seqNameForBam, winStart, winEnd);
 
 struct hash *pairHash = isPaired ? hashNew(0) : NULL;
 struct bamTrackData btd = {start, item, pairHash};
 bamFetch(database, tdb->tableName, posForBam, oneBam, &btd);
 if (isPaired)
     {
     struct hashEl *hel;
     struct hashCookie cookie = hashFirst(pairHash);
     while ((hel = hashNext(&cookie)) != NULL)
 	{
 	// uh-oh -- we need to search for the mate.
+	uglyf("<B>Note: paired end not shown (zoom out or bug Angie to fix code):</B><BR>\n");
+	singleBamDetails((bam1_t *)hel->val);
 	}
     }
 }
 
 #endif//def USE_BAM