Renamed makefile as Makefile

[rsem.git] / BamWriter.h

diff --git a/BamWriter.h b/BamWriter.h
index 733eaeffacb924b227fa437d5c9e88976c3e6545..2a325d6cb46901760ef1cebe01b5cbbba1136ee7 100644 (file)
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -55,9 +55,6 @@ BamWriter::BamWriter(char inpType, const char* inpF, const char* fn_list, const
 
        //generate output's header
        bam_header_t *out_header = bam_header_dwt(in->header);
-       for (int i = 0; i < out_header->n_targets; i++) {
-               out_header->target_len[i] = transcripts.getTranscriptViaEid(i + 1).getLength();  // transcript length without poly(A) tail
-       }
 
        std::ostringstream strout;
        strout<<"@HD\tVN:1.4\tSO:unknown\n@PG\tID:RSEM\n";
@@ -109,14 +106,14 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
        bam1_t *b, *b2;
        PairedEndHit *hit;
 
-       int cnt = 0;
+       HIT_INT_TYPE cnt = 0;
 
        b = bam_init1();
        b2 = bam_init1();
 
        while (samread(in, b) >= 0 && samread(in, b2) >= 0) {
                cnt += 2;
-               if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< "alignment lines are loaded!"<< std::endl; }
+               if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< " alignment lines are loaded!"<< std::endl; }
 
                assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001));
                assert(((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) || ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)));
@@ -140,22 +137,9 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 
                        convert(b, hit->getConPrb());
                        convert(b2, hit->getConPrb());
-               }
 
-               /*
-               else {
-                 // if only one mate can be aligned, mask it as unaligned and put an additional tag Z0:A:!
-                 char exclamation = '!';
-                 if (!(b->core.flag & 0x0004)) { 
-                   b->core.flag |= 0x0004;
-                   bam_aux_append(b, "Z0", 'A', bam_aux_type2size('A'), (uint8_t*)&exclamation);
-                 }
-                 if (!(b2->core.flag & 0x0004)) {
-                   b2->core.flag |= 0x0004;
-                   bam_aux_append(b2, "Z0", 'A', bam_aux_type2size('A'), (uint8_t*)&exclamation);
-                 }
+                       // omit "b->core.mpos = b2->core.pos; b2->core.mpos = b->core.pos" for the reason that it is possible that only one mate is alignable 
                }
-               */
 
                samwrite(out, b);
                samwrite(out, b2);