e88c50da16cb4c6b62702cd9440b12e2dae174de
braney
  Wed Feb 17 12:28:45 2016 -0800
fix gff3ToPsl to get the strands right

diff --git src/lib/psl.c src/lib/psl.c
index 23f921f..d30be8a 100644
--- src/lib/psl.c
+++ src/lib/psl.c
@@ -1928,34 +1928,34 @@
     // no cigar means one block
     size = qEnd - qStart;
     totalSize += size;
     psl->blockSizes[psl->blockCount] = size;
     psl->qStarts[psl->blockCount] = qNext;
     psl->tStarts[psl->blockCount] = tNext;
     psl->blockCount++;
     tNext += size;
     qNext += size;
     }
 else
     {
     char cigarSpec[strlen(cigar+1)];  // copy since parsing is destructive
     strcpy(cigarSpec, cigar);
     char *cigarNext = cigarSpec;
-    if (strand[0] == '-')
+    if (strand[1] == '-')
 	for(; *cigarNext; cigarNext++)
 	    ;
-    while(getNextCigarOp(cigarSpec, (strand[0] == '-'), &cigarNext, &op, &size))
+    while(getNextCigarOp(cigarSpec, (strand[1] == '-'), &cigarNext, &op, &size))
 	{
 	switch (op)
 	    {
 	    case 'M': // match or mismatch (gapless aligned block)
 		if (psl->blockCount == blocksAlloced)
 		    pslGrow(psl, &blocksAlloced);
 
 		totalSize += size;
 		psl->blockSizes[psl->blockCount] = size;
 		psl->qStarts[psl->blockCount] = qNext;
 		psl->tStarts[psl->blockCount] = tNext;
 		psl->blockCount++;
 		tNext += size;
 		qNext += size;
 		break;