0f28f57729ca94d504f5dd4cf9f2704b8089dac3
markd
  Sun Aug 16 21:59:23 2015 -0400
converted macro to access PSL strands to inline functions to improve code reliablity (no redmine)

diff --git src/inc/psl.h src/inc/psl.h
index 894e3d7..c9a9d1d 100644
--- src/inc/psl.h
+++ src/inc/psl.h
@@ -185,34 +185,42 @@
 struct ffAli *pslToFakeFfAli(struct psl *psl, DNA *needle, DNA *haystack);
 /* Convert from psl to ffAli format.  In some cases you can pass NULL
  * for needle and haystack - depending what the post-processing is going
  * to be. */
 
 struct psl *pslFromFakeFfAli(struct ffAli *ff, 
 	DNA *needle, DNA *haystack, char strand,
 	char *qName, int qSize, char *tName, int tSize);
 /* This will create a basic psl structure from a sorted series of ffAli
  * blocks.  The fields that would need actual sequence to be filled in
  * are left zero however - fields including match, repMatch, mismatch. */
 
 int pslOrientation(struct psl *psl);
 /* Translate psl strand + or - to orientation +1 or -1 */
 
-/* marcos to get query and target strand.  Target returns implied + when
+INLINE char pslQStrand(struct psl *psl)
+/* Get query strand. */
+{
+return psl->strand[0];
+}
+
+INLINE char pslTStrand(struct psl *psl)
+/* Get the target strand., Returns implied + when
  * it's not specific  */
-#define pslQStrand(p) ((p)->strand[0])
-#define pslTStrand(p) (((p)->strand[1] != '-') ? '+' : '-')
+{
+return (psl->strand[1] != '-') ? '+' : '-';
+}
 
 int pslWeightedIntronOrientation(struct psl *psl, struct dnaSeq *genoSeq, int offset);
 /* Return >0 if introns make it look like alignment is on + strand,
  *        <0 if introns make it look like alignment is on - strand,
  *        0 if can't tell.  The absolute value of the return indicates
  * how many splice sites we've seen supporting the orientation.
  * Sequence should NOT be reverse complemented.  */
 
 int pslIntronOrientation(struct psl *psl, struct dnaSeq *genoSeq, int offset);
 /* Return 1 if introns make it look like alignment is on + strand,
  *       -1 if introns make it look like alignment is on - strand,
  *        0 if can't tell.
  * Sequence should NOT be reverse complemented.  */
 
 boolean pslHasIntron(struct psl *psl, struct dnaSeq *seq, int seqOffset);