use if/elsif to replace switch in rsem-calculate-expression

[rsem.git] / BamWriter.h

diff --git a/BamWriter.h b/BamWriter.h
index 8c568f348f361fd009c964cd2b9ad021e50fc257..733eaeffacb924b227fa437d5c9e88976c3e6545 100644 (file)
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -119,7 +119,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
                if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< "alignment lines are loaded!"<< std::endl; }
 
                assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001));
-               assert((b->core.flag & 0x0040) && (b2->core.flag & 0x0080) || (b->core.flag & 0x0080) && (b2->core.flag & 0x0040));
+               assert(((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) || ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)));
 
                //unalignable reads, skip               
                bool notgood = (b->core.flag & 0x0004) || (b2->core.flag & 0x0004);
@@ -140,9 +140,6 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 
                        convert(b, hit->getConPrb());
                        convert(b2, hit->getConPrb());
-
-                       b->core.mpos = b2->core.pos;
-                       b2->core.mpos = b->core.pos;
                }
 
                /*