The order of @SQ tags in SAM/BAM files can be arbitrary now

[rsem.git] / BamConverter.h

diff --git a/BamConverter.h b/BamConverter.h
index e7253ba9415b566442f3efbfe266ffe052bb2753..af984ac4968c24a6a0c297154374bdaa32dbcd9e 100644 (file)
--- a/BamConverter.h
+++ b/BamConverter.h
@@ -50,6 +50,8 @@ BamConverter::BamConverter(const char* inpF, const char* outF, const char* chr_l
        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) {