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
  59         std::ostringstream strout;
  60         strout<<"@HD\tVN:1.4\tSO:unknown\n@PG\tID:RSEM\n";
  61         std::string content = strout.str();
  62         append_header_text(out_header, content.c_str(), content.length());
  63
  64         out = samopen(outF, "wb", out_header);
  65         assert(out != 0);
  66
  67         bam_header_destroy(out_header);
  68 }
  69
  70 BamWriter::~BamWriter() {
  71         samclose(in);
  72         samclose(out);
  73 }
  74
  75 void BamWriter::work(HitWrapper<SingleHit> wrapper) {
  76         bam1_t *b;
  77         SingleHit *hit;
  78
  79         HIT_INT_TYPE cnt = 0;
  80
  81         b = bam_init1();
  82
  83         while (samread(in, b) >= 0) {
  84                 ++cnt;
  85                 if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< " alignment lines are loaded!"<< std::endl; }
  86
  87                 if (!(b->core.flag & 0x0004)) {
  88                   hit = wrapper.getNextHit();
  89                   assert(hit != NULL);
  90
  91                   assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
  92                   convert(b, hit->getConPrb());
  93                 }
  94
  95                 //if (b->core.qual > 0) samwrite(out, b); // output only when MAPQ > 0
  96                 samwrite(out, b);
  97         }
  98
  99         assert(wrapper.getNextHit() == NULL);
 100
 101         bam_destroy1(b);
 102         if (verbose) { std::cout<< "Bam output file is generated!"<< std::endl; }
 103 }
 104
 105 void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 106         bam1_t *b, *b2;
 107         PairedEndHit *hit;
 108
 109         HIT_INT_TYPE cnt = 0;
 110
 111         b = bam_init1();
 112         b2 = bam_init1();
 113
 114         while (samread(in, b) >= 0 && samread(in, b2) >= 0) {
 115                 cnt += 2;
 116                 if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< " alignment lines are loaded!"<< std::endl; }
 117
 118                 assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001));
 119                 assert(((b->core.flag & 0x0040) && (b2->core.flag & 0x0080)) || ((b->core.flag & 0x0080) && (b2->core.flag & 0x0040)));
 120
 121                 //unalignable reads, skip
 122                 bool notgood = (b->core.flag & 0x0004) || (b2->core.flag & 0x0004);
 123
 124                 if (!notgood) {
 125                         //swap if b is mate 2
 126                         if (b->core.flag & 0x0080) {
 127                                 assert(b2->core.flag & 0x0040);
 128                                 bam1_t *tmp = b;
 129                                 b = b2; b2 = tmp;
 130                         }
 131
 132                         hit = wrapper.getNextHit();
 133                         assert(hit != NULL);
 134
 135                         assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
 136                         assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
 137
 138                         convert(b, hit->getConPrb());
 139                         convert(b2, hit->getConPrb());
 140
 141                         // 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
 142                 }
 143
 144                 samwrite(out, b);
 145                 samwrite(out, b2);
 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         b->core.qual = getMAPQ(prb);
 158         float val = (float)prb;
 159         bam_aux_append(b, "ZW", 'f', bam_aux_type2size('f'), (uint8_t*)&val);
 160 }
 161
 162 #endif /* BAMWRITER_H_ */