Renamed makefile as Makefile

[rsem.git] / BamWriter.h

diff --git a/BamWriter.h b/BamWriter.h
index f664710245ff265e184f922c642c0d3efc74a29a..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";
@@ -109,56 +106,40 @@ 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));
+               assert(((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) || ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)));
 
                //unalignable reads, skip               
                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;
-                 }
-
-                 hit = wrapper.getNextHit();
-                 assert(hit != NULL);
+                       //swap if b is mate 2
+                       if (b->core.flag & 0x0080) {
+                               assert(b2->core.flag & 0x0040);
+                               bam1_t *tmp = b;
+                               b = b2; b2 = tmp;
+                       }
 
-                 assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
-                 assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
+                       hit = wrapper.getNextHit();
+                       assert(hit != NULL);
 
-                 convert(b, hit->getConPrb());
-                 convert(b2, hit->getConPrb());
+                       assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
+                       assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
 
-                 b->core.mpos = b2->core.pos;
-                 b2->core.mpos = b->core.pos;
-               }
+                       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);
@@ -173,33 +154,7 @@ 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);
 }