src/hg/lib/bamFile.c 1.4

Index: src/hg/lib/bamFile.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/bamFile.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/lib/bamFile.c	3 Aug 2009 22:14:39 -0000	1.3
+++ src/hg/lib/bamFile.c	21 Aug 2009 05:22:01 -0000	1.4
@@ -115,5 +115,54 @@
     }
 return tLength;
 }
 
+struct ffAli *bamToFfAli(const bam1_t *bam, struct dnaSeq *target, int targetOffset)
+/* Convert from bam to ffAli format.  (Adapted from psl.c's pslToFfAli.) */
+{
+struct ffAli *ffList = NULL, *ff;
+const bam1_core_t *core = &bam->core;
+boolean isRc = ((core->flag & BAM_FREVERSE) != 0);
+DNA *needle = (DNA *)bamGetQuerySequence(bam);
+if (isRc)
+    reverseComplement(needle, strlen(needle));
+DNA *haystack = target->dna;
+unsigned int *cigarPacked = bam1_cigar(bam);
+int tStart, qStart, i;
+for (tStart = targetOffset, qStart = 0, i = 0;  i < core->n_cigar;  i++)
+    {
+    char op;
+    int size = bamUnpackCigarElement(cigarPacked[i], &op);
+    switch (op)
+	{
+	case 'M': // match or mismatch (gapless aligned block)
+	    AllocVar(ff);
+	    ff->left = ffList;
+	    ffList = ff;
+	    ff->nStart = needle + qStart;
+	    ff->nEnd = ff->nStart + size;
+	    ff->hStart = haystack + tStart - targetOffset;
+	    ff->hEnd = ff->hStart + size;
+	    tStart += size;
+	    qStart += size;
+	    break;
+	case 'I': // inserted in query
+	case 'S': // skipped query bases at beginning or end ("soft clipping")
+	    qStart += size;
+	    break;
+	case 'D': // deleted from query
+	case 'N': // long deletion from query (intron as opposed to small del)
+	    tStart += size;
+	    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("bamToFfAli: unrecognized CIGAR op %c -- update me", op);
+	}
+    }
+ffList = ffMakeRightLinks(ffList);
+ffCountGoodEnds(ffList);
+return ffList;
+}
+
 #endif//def USE_BAM