Added --version option for rsem-calculate-expression

[rsem.git] / BamConverter.h

diff --git a/BamConverter.h b/BamConverter.h
index 13b8557f5bc727916ba31857cfdd39ac839d39d0..320824b5f93a266d3e451dc4ec3a757c4a1dadd4 100644 (file)
--- a/BamConverter.h
+++ b/BamConverter.h
@@ -87,7 +87,7 @@ void BamConverter::process() {
                if (isPaired) {
                        assert(samread(in, b2) >= 0 && (b2->core.flag & 0x0001));
                        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)));
                        ++cnt;
                }
 
@@ -101,7 +101,7 @@ void BamConverter::process() {
 
 
                if (!notgood) {
-                 assert((b->core.tid == b2->core.tid) && (b->core.flag & 0x0040) && (b2->core.flag & 0x0080)); // for collapsing
+                 if (isPaired) assert((b->core.tid == b2->core.tid) && (b->core.flag & 0x0040) && (b2->core.flag & 0x0080)); // for collapsing
 
                  const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);