X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamWriter.h;h=b39400f5cb9d21c50d2dcdf8ac0222218c5f2286;hb=791b978145b0d22865ee350db9d58072bb99d816;hp=7f3c562309678389e6f98aae29addce776110939;hpb=a95154919f950f86de9104b2b9dcf1f0c7e83387;p=rsem.git

diff --git a/BamWriter.h b/BamWriter.h
index 7f3c562..b39400f 100644
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -174,6 +174,7 @@ BamWriter::BamWriter(char inpType, const char* inpF, const char* fn_list, const
 		}
 	}
 
+
 	out = samopen(outF, "wb", out_header);
 	assert(out != 0);
 
@@ -226,7 +227,7 @@ void BamWriter::work(HitWrapper<SingleHit> wrapper, Transcripts& transcripts) {
 
 			uint16_t rstrand = b->core.flag & 0x0010; // read strand
 			b->core.flag -= rstrand;
-			rstrand = (!rstrand && transcript.getStrand() == '+' || rstrand && transcript.getStrand() == '-' ? 0 : 0x0010);
+			rstrand = (((!rstrand && transcript.getStrand() == '+') || (rstrand && transcript.getStrand() == '-')) ? 0 : 0x0010);
 			b->core.flag += rstrand;
 
 			push_qname(qname, b->core.l_qname, data);
@@ -355,7 +356,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper, Transcripts& transcripts)
 			b2->core.flag = b2->core.flag - (b2->core.flag & 0x0010) - (b2->core.flag & 0x0020);
 
 			uint16_t add, add2;
-			if (!rstrand && transcript.getStrand() == '+' || rstrand && transcript.getStrand() == '-') {
+			if ((!rstrand && transcript.getStrand() == '+') || (rstrand && transcript.getStrand() == '-')) {
 				add = 0x0020; add2 = 0x0010;
 			}
 			else {
@@ -478,7 +479,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper, Transcripts& transcripts)
 	bam_destroy1(b);
 	bam_destroy1(b2);
 
-	if (verbose) { printf("Bam output file is generated!"); }
+	if (verbose) { printf("Bam output file is generated!\n"); }
 }
 
 void BamWriter::tr2chr(const Transcript& transcript, int sp, int ep, int& pos, int& n_cigar, std::vector<uint8_t>& data) {