X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamWriter.h;h=8c568f348f361fd009c964cd2b9ad021e50fc257;hb=7bbb1f6e5c87e6a953789c1f3ef49d3ce891e31e;hp=782f5bdeb6705748a8919265e854b54d1f418133;hpb=509ffe2d71cf6a6f5cca8c39909f8ee10b8db899;p=rsem.git

diff --git a/BamWriter.h b/BamWriter.h
index 782f5bd..8c568f3 100644
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -125,25 +125,27 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 		bool notgood = (b->core.flag & 0x0004) || (b2->core.flag & 0x0004);
 
 		if (!notgood) {
-		  //swap if b is mate 2
-		  if (b->core.flag & 0x0080) {
-		    assert(b2->core.flag & 0x0040);
-		    bam1_t *tmp = b;
-		    b = b2; b2 = tmp;
-		  }
+			//swap if b is mate 2
+			if (b->core.flag & 0x0080) {
+				assert(b2->core.flag & 0x0040);
+				bam1_t *tmp = b;
+				b = b2; b2 = tmp;
+			}
 
-		  hit = wrapper.getNextHit();
-		  assert(hit != NULL);
+			hit = wrapper.getNextHit();
+			assert(hit != NULL);
 
-		  assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
-		  assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
+			assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
+			assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
 
-		  convert(b, hit->getConPrb());
-		  convert(b2, hit->getConPrb());
+			convert(b, hit->getConPrb());
+			convert(b2, hit->getConPrb());
 
-		  b->core.mpos = b2->core.pos;
-		  b2->core.mpos = b->core.pos;
+			b->core.mpos = b2->core.pos;
+			b2->core.mpos = b->core.pos;
 		}
+
+		/*
 		else {
 		  // if only one mate can be aligned, mask it as unaligned and put an additional tag Z0:A:!
 		  char exclamation = '!';
@@ -156,7 +158,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 		    bam_aux_append(b2, "Z0", 'A', bam_aux_type2size('A'), (uint8_t*)&exclamation);
 		  }
 		}
-
+		*/
 
 		samwrite(out, b);
 		samwrite(out, b2);
@@ -171,33 +173,7 @@ void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 }
 
 void BamWriter::convert(bam1_t *b, double prb) {
-	const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);
-
-	int pos = b->core.pos;
-	int readlen = b->core.l_qseq;
-
-	std::vector<uint32_t> data;
-	data.clear();
-
-	int core_pos, core_n_cigar;
-	std::vector<Interval> vec;
-	vec.assign(1, Interval(1, transcript.getLength()));
-	// make an artificial chromosome coordinates for the transcript to get new CIGAR strings
-	tr2chr(Transcript("", "", "", '+', vec, ""), pos + 1, pos + readlen, core_pos, core_n_cigar, data);
-	assert(core_pos >= 0);
-
-	int rest_len = b->data_len - b->core.l_qname - b->core.n_cigar * 4;
-	b->data_len = b->core.l_qname + core_n_cigar * 4 + rest_len;
-	expand_data_size(b);
-	uint8_t* pt = b->data + b->core.l_qname;
-	memmove(pt + core_n_cigar * 4, pt + b->core.n_cigar * 4, rest_len);
-	for (int i = 0; i < core_n_cigar; i++) { memmove(pt, &data[i], 4); pt += 4; }
-
-	b->core.pos = core_pos;
-	b->core.n_cigar = core_n_cigar;
 	b->core.qual = getMAPQ(prb);
-	b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&(b->core), bam1_cigar(b)));
-
 	float val = (float)prb;
 	bam_aux_append(b, "ZW", 'f', bam_aux_type2size('f'), (uint8_t*)&val);
 }