53b5272717c4018db1917c5a5f9453d4780804b2
markd
  Sun Aug 16 22:02:43 2015 -0400
added inline function to get PSL block starts to match ones to get block ends (no redmine)

diff --git src/inc/psl.h src/inc/psl.h
index c9a9d1d..ef54630 100644
--- src/inc/psl.h
+++ src/inc/psl.h
@@ -296,30 +296,42 @@
 
 struct psl* pslFromGff3Cigar(char *qName, int qSize, int qStart, int qEnd,
                              char *tName, int tSize, int tStart, int tEnd,
                              char* strand, char *cigar);
 /* create a PSL from a GFF3-style cigar formatted alignment */
 
 int pslRangeTreeOverlap(struct psl *psl, struct rbTree *rangeTree);
 /* Return amount that psl overlaps (on target side) with rangeTree. */
 
 float pslIdent(struct psl *psl);
 /* computer fraction identity */
 
 float pslQueryAligned(struct psl *psl);
 /* compute fraction of query that was aligned */
 
+INLINE unsigned pslQStart(struct psl *psl, int blkIdx)
+/* return query start for the given block */
+{
+return psl->qStarts[blkIdx];
+}
+
+INLINE unsigned pslTStart(struct psl *psl, int blkIdx)
+/* return target start for the given block */
+{
+return psl->tStarts[blkIdx];
+}
+
 INLINE unsigned pslQEnd(struct psl *psl, int blkIdx)
 /* return query end for the given block */
 {
 return psl->qStarts[blkIdx] + psl->blockSizes[blkIdx];
 }
 
 INLINE unsigned pslTEnd(struct psl *psl, int blkIdx)
 /* return target end for the given block */
 {
 return psl->tStarts[blkIdx] + psl->blockSizes[blkIdx];
 }
 
 struct psl* pslClone(struct psl *psl);
 /* clone a psl */