BamWriter.h

   1 #ifndef BAMWRITER_H_
   2 #define BAMWRITER_H_
   3
   4 #include<cmath>
   5 #include<cstdio>
   6 #include<cstring>
   7 #include<cassert>
   8 #include<string>
   9 #include<sstream>
  10 #include<iostream>
  11
  12 #include <stdint.h>
  13 #include "sam/bam.h"
  14 #include "sam/sam.h"
  15 #include "sam_rsem_aux.h"
  16 #include "sam_rsem_cvt.h"
  17
  18 #include "utils.h"
  19
  20 #include "SingleHit.h"
  21 #include "PairedEndHit.h"
  22
  23 #include "HitWrapper.h"
  24 #include "Transcript.h"
  25 #include "Transcripts.h"
  26
  27 class BamWriter {
  28 public:
  29         BamWriter(char, const char*, const char*, const char*, Transcripts&);
  30         ~BamWriter();
  31
  32         void work(HitWrapper<SingleHit>);
  33         void work(HitWrapper<PairedEndHit>);
  34 private:
  35         samfile_t *in, *out;
  36         Transcripts& transcripts;
  37
  38         //convert bam1_t
  39         void convert(bam1_t*, double);
  40 };
  41
  42 //fn_list can be NULL
  43 BamWriter::BamWriter(char inpType, const char* inpF, const char* fn_list, const char* outF, Transcripts& transcripts)
  44         : transcripts(transcripts)
  45 {
  46         switch(inpType) {
  47         case 's': in = samopen(inpF, "r", fn_list); break;
  48         case 'b': in = samopen(inpF, "rb", fn_list); break;
  49         default: assert(false);
  50         }
  51         assert(in != 0);
  52
  53         //build mappings from external sid to internal sid
  54         transcripts.buildMappings(in->header->n_targets, in->header->target_name);
  55
  56         //generate output's header
  57         bam_header_t *out_header = bam_header_dwt(in->header);
  58         for (int i = 0; i < out_header->n_targets; i++) {
  59                 out_header->target_len[i] = transcripts.getTranscriptViaEid(i + 1).getLength();  // transcript length without poly(A) tail
  60         }
  61
  62         std::ostringstream strout;
  63         strout<<"@HD\tVN:1.4\tSO:unknown\n@PG\tID:RSEM\n";
  64         std::string content = strout.str();
  65         append_header_text(out_header, content.c_str(), content.length());
  66
  67         out = samopen(outF, "wb", out_header);
  68         assert(out != 0);
  69
  70         bam_header_destroy(out_header);
  71 }
  72
  73 BamWriter::~BamWriter() {
  74         samclose(in);
  75         samclose(out);
  76 }
  77
  78 void BamWriter::work(HitWrapper<SingleHit> wrapper) {
  79         bam1_t *b;
  80         SingleHit *hit;
  81
  82         HIT_INT_TYPE cnt = 0;
  83
  84         b = bam_init1();
  85
  86         while (samread(in, b) >= 0) {
  87                 ++cnt;
  88                 if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< "alignment lines are loaded!"<< std::endl; }
  89
  90                 if (b->core.flag & 0x0004) continue;
  91
  92                 hit = wrapper.getNextHit();
  93                 assert(hit != NULL);
  94
  95                 assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
  96                 convert(b, hit->getConPrb());
  97                 if (b->core.qual > 0) samwrite(out, b); // output only when MAPQ > 0
  98         }
  99
 100         assert(wrapper.getNextHit() == NULL);
 101
 102         bam_destroy1(b);
 103         if (verbose) { std::cout<< "Bam output file is generated!"<< std::endl; }
 104 }
 105
 106 void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 107         bam1_t *b, *b2;
 108         PairedEndHit *hit;
 109
 110         int cnt = 0;
 111
 112         b = bam_init1();
 113         b2 = bam_init1();
 114
 115         while (samread(in, b) >= 0 && samread(in, b2) >= 0) {
 116                 cnt += 2;
 117                 if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< "alignment lines are loaded!"<< std::endl; }
 118                 //mate info is not complete, skip
 119                 if (!(((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) || ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)))) continue;
 120                 //unalignable reads, skip
 121                 if ((b->core.flag & 0x0004) || (b2->core.flag & 0x0004)) continue;
 122
 123                 //swap if b is mate 2
 124                 if (b->core.flag & 0x0080) {
 125                         assert(b2->core.flag & 0x0040);
 126                         bam1_t *tmp = b;
 127                         b = b2; b2 = tmp;
 128                 }
 129
 130                 hit = wrapper.getNextHit();
 131                 assert(hit != NULL);
 132
 133                 assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
 134                 assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
 135
 136                 convert(b, hit->getConPrb());
 137                 convert(b2, hit->getConPrb());
 138
 139                 b->core.mpos = b2->core.pos;
 140                 b2->core.mpos = b->core.pos;
 141
 142                 if (b->core.qual > 0) {
 143                         samwrite(out, b);
 144                         samwrite(out, b2);
 145                 }
 146         }
 147
 148         assert(wrapper.getNextHit() == NULL);
 149
 150         bam_destroy1(b);
 151         bam_destroy1(b2);
 152
 153         if (verbose) { std::cout<< "Bam output file is generated!"<< std::endl; }
 154 }
 155
 156 void BamWriter::convert(bam1_t *b, double prb) {
 157         const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);
 158
 159         int pos = b->core.pos;
 160         int readlen = b->core.l_qseq;
 161
 162         std::vector<uint32_t> data;
 163         data.clear();
 164
 165         int core_pos, core_n_cigar;
 166         std::vector<Interval> vec;
 167         vec.assign(1, Interval(1, transcript.getLength()));
 168         // make an artificial chromosome coordinates for the transcript to get new CIGAR strings
 169         tr2chr(Transcript("", "", "", '+', vec, ""), pos + 1, pos + readlen, core_pos, core_n_cigar, data);
 170         assert(core_pos >= 0);
 171
 172         int rest_len = b->data_len - b->core.l_qname - b->core.n_cigar * 4;
 173         b->data_len = b->core.l_qname + core_n_cigar * 4 + rest_len;
 174         expand_data_size(b);
 175         uint8_t* pt = b->data + b->core.l_qname;
 176         memmove(pt + core_n_cigar * 4, pt + b->core.n_cigar * 4, rest_len);
 177         for (int i = 0; i < core_n_cigar; i++) { memmove(pt, &data[i], 4); pt += 4; }
 178
 179         b->core.pos = core_pos;
 180         b->core.n_cigar = core_n_cigar;
 181         b->core.qual = getMAPQ(prb);
 182         b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&(b->core), bam1_cigar(b)));
 183
 184         float val = (float)prb;
 185         bam_aux_append(b, "ZW", 'f', bam_aux_type2size('f'), (uint8_t*)&val);
 186 }
 187
 188 #endif /* BAMWRITER_H_ */