#include "sam_rsem_cvt.h"
#include "utils.h"
+#include "my_assert.h"
#include "bc_aux.h"
#include "Transcript.h"
#include "Transcripts.h"
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);
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());