src/hg/lib/bamFile.c 1.5

Index: src/hg/lib/bamFile.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/bamFile.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/hg/lib/bamFile.c	21 Aug 2009 05:22:01 -0000	1.4
+++ src/hg/lib/bamFile.c	21 Aug 2009 22:52:35 -0000	1.5
@@ -123,13 +123,16 @@
 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));
+    reverseComplement(target->dna, target->size);
 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++)
+int tStart = targetOffset, qStart = 0, i;
+// If isRc, need to go through the CIGAR ops backwards, but sequence offsets still count up.
+int iStart = isRc ? (core->n_cigar - 1) : 0;
+int iIncr = isRc ? -1 : 1;
+for (i = iStart;  isRc ? (i >= 0) : (i < core->n_cigar);  i += iIncr)
     {
     char op;
     int size = bamUnpackCigarElement(cigarPacked[i], &op);
     switch (op)
@@ -164,5 +167,14 @@
 ffCountGoodEnds(ffList);
 return ffList;
 }
 
+bam1_t *bamClone(const bam1_t *bam)
+/* Return a newly allocated copy of bam. */
+{
+// Using typecasts to get around compiler complaints about bam being const:
+bam1_t *newBam = cloneMem((void *)bam, sizeof(*bam));
+newBam->data = cloneMem((void *)bam->data, bam->data_len*sizeof(bam->data[0]));
+return newBam;
+}
+
 #endif//def USE_BAM