src/hg/hgc/bamClick.c 1.2

Index: src/hg/hgc/bamClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/bamClick.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/hgc/bamClick.c	28 Jul 2009 15:57:40 -0000	1.1
+++ src/hg/hgc/bamClick.c	3 Aug 2009 22:00:24 -0000	1.2
@@ -1,137 +1,96 @@
 /* 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 int lengthFromNumericCigar(const bam1_t *bam)
-/* Translate BAM's numeric CIGAR encoding into length on reference. */
-{
-const bam1_core_t *core = &bam->core;
-int tLength=0;
-unsigned int *cigar = bam1_cigar(bam);
-int i;
-for (i = 0;  i < core->n_cigar;  i++)
-    {
-//TODO: libify the nasty part here, shared w/hgTracks/bamTrack.c
-    // decoding lifted from bam.c bam_format1(), long may it remain stable:
-    int n = cigar[i]>>BAM_CIGAR_SHIFT;
-    int opcode = cigar[i] & BAM_CIGAR_MASK;
-    char op = "MIDNSHP"[opcode];
-    switch (op)
-	{
-	case 'M': // match or mismatch (gapless aligned block)
-	    tLength += n;
-	    break;
-	case 'I': // inserted in query
-	case 'S': // skipped query bases at beginning or end ("soft clipping")
-	    break;
-	case 'D': // deleted from query
-	case 'N': // long deletion from query (intron as opposed to small del)
-	    tLength += n;
-	    break;
-	case 'H': // skipped query bases not stored in record's query sequence ("hard clipping")
-	case 'P': // P="silent deletion from padded reference sequence" -- ignore these.
-	    break;
-	default:
-	    errAbort("Unrecognized CIGAR op index %d -- has bam.c bam_format1() changed?", opcode);
-	}
-    }
-return tLength;
-}
-
 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 length = lengthFromNumericCigar(bam);
+int length = bamGetTargetLength(bam);
 printPosOnChrom(seqName, core->pos, core->pos+length, (core->flag & BAM_FREVERSE) ? "-" : "+",
 		FALSE, itemName);
-char *qSeq = needMem(core->l_qseq + 1);
-uint8_t *s = bam1_seq(bam);
-int i;
-for (i = 0; i < core->l_qseq; i++)
-    qSeq[i] = bam_nt16_rev_table[bam1_seqi(s, i)];
-if ((core->flag & BAM_FREVERSE) == 1)
-    reverseComplement(qSeq, core->l_qseq);
+printf("<B>CIGAR string: </B><tt>%s</tt><BR>\n", bamGetCigar(bam));
+char *qSeq = bamGetQuerySequence(bam);
 printf("<B>Read Sequence: </B><tt>%s</tt><BR>\n", qSeq);
 //TODO: show flags, display alignment properly, maybe display quality scores
 }
 
 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.
 	}
     }
 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.
 	}
     }
 }
 
 #endif//def USE_BAM