X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamConverter.h;h=af984ac4968c24a6a0c297154374bdaa32dbcd9e;hb=97554bbac838f2ed578d81f98e421dac0669e74e;hp=cca0eae895fd347b243cc8f2f315be471c64498c;hpb=0a534802ee9fa3d488995a68621ff04f0fc6be7f;p=rsem.git

diff --git a/BamConverter.h b/BamConverter.h
index cca0eae..af984ac 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"
@@ -44,12 +45,13 @@ 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);
 
+	transcripts.buildMappings(in->header->n_targets, in->header->target_name);
+
 	bam_header_t *out_header = sam_header_read2(chr_list);
 	refmap.clear();
 	for (int i = 0; i < out_header->n_targets; i++) {
@@ -93,7 +95,7 @@ void BamConverter::process() {
 		// at least one segment is not properly mapped
 		if ((b->core.flag & 0x0004) || (isPaired && (b2->core.flag & 0x0004))) continue;
 
-		const Transcript& transcript = transcripts.getTranscriptAt(b->core.tid + 1);
+		const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);
 
 		convert(b, transcript);
 		if (isPaired) {
@@ -123,7 +125,7 @@ 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());