X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamConverter.h;h=e7253ba9415b566442f3efbfe266ffe052bb2753;hb=cb94fd597b180aa7cb01ae84c9d1025201b98d8e;hp=9b543087443aac68a72999a13e874b199d613cc4;hpb=5fd66ada6c610981dcecd50e5e41436e0458b110;p=rsem.git

diff --git a/BamConverter.h b/BamConverter.h
index 9b54308..e7253ba 100644
--- a/BamConverter.h
+++ b/BamConverter.h
@@ -14,6 +14,7 @@
 #include "sam_rsem_cvt.h"
 
 #include "utils.h"
+#include "my_assert.h"
 #include "bc_aux.h"
 #include "Transcript.h"
 #include "Transcripts.h"
@@ -44,8 +45,7 @@ private:
 BamConverter::BamConverter(const char* inpF, const char* outF, const char* chr_list, Transcripts& transcripts)
 	: transcripts(transcripts)
 {
-	if (transcripts.getType() != 0)
-		exitWithError("Genome information is not provided! RSEM cannot convert the transcript bam file!");
+	general_assert(transcripts.getType() == 0, "Genome information is not provided! RSEM cannot convert the transcript bam file!");
 
 	in = samopen(inpF, "rb", NULL);
 	assert(in != 0);
@@ -91,7 +91,7 @@ void BamConverter::process() {
 		if (cnt % 1000000 == 0) { printf("."); fflush(stdout); }
 
 		// at least one segment is not properly mapped
-		if ((b->core.flag & 0x0004) || isPaired && (b2->core.flag & 0x0004)) continue;
+		if ((b->core.flag & 0x0004) || (isPaired && (b2->core.flag & 0x0004))) continue;
 
 		const Transcript& transcript = transcripts.getTranscriptAt(b->core.tid + 1);
 
@@ -123,7 +123,7 @@ void BamConverter::convert(bam1_t* b, const Transcript& transcript) {
 	int pos = b->core.pos;
 	int readlen = b->core.l_qseq;
 
-	if (readlen == 0) exitWithError("One alignment line has SEQ field as *. RSEM does not support this currently!");
+	general_assert(readlen > 0, "One alignment line has SEQ field as *. RSEM does not support this currently!");
 
 	iter = refmap.find(transcript.getSeqName());
 	assert(iter != refmap.end());