add --no-bam-output option to not generate output bam files

[rsem.git] / BamConverter.h

diff --git a/BamConverter.h b/BamConverter.h
index 9b543087443aac68a72999a13e874b199d613cc4..e7253ba9415b566442f3efbfe266ffe052bb2753 100644 (file)
--- 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());