X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamConverter.h;h=320824b5f93a266d3e451dc4ec3a757c4a1dadd4;hb=0165dcc248203dce454881b6f1707cdf248497c2;hp=13b8557f5bc727916ba31857cfdd39ac839d39d0;hpb=509ffe2d71cf6a6f5cca8c39909f8ee10b8db899;p=rsem.git

diff --git a/BamConverter.h b/BamConverter.h
index 13b8557..320824b 100644
--- 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);