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
  11 #include <stdint.h>
  12 #include "sam/bam.h"
  13 #include "sam/sam.h"
  14 #include "sam_rsem_aux.h"
  15 #include "sam_rsem_cvt.h"
  16
  17 #include "SingleHit.h"
  18 #include "PairedEndHit.h"
  19
  20 #include "HitWrapper.h"
  21 #include "Transcript.h"
  22 #include "Transcripts.h"
  23
  24 class BamWriter {
  25 public:
  26         BamWriter(char, const char*, const char*, const char*, Transcripts&);
  27         ~BamWriter();
  28
  29         void work(HitWrapper<SingleHit>);
  30         void work(HitWrapper<PairedEndHit>);
  31 private:
  32         samfile_t *in, *out;
  33         Transcripts& transcripts;
  34
  35         //convert bam1_t
  36         void convert(bam1_t*, double);
  37 };
  38
  39 //fn_list can be NULL
  40 BamWriter::BamWriter(char inpType, const char* inpF, const char* fn_list, const char* outF, Transcripts& transcripts)
  41         : transcripts(transcripts)
  42 {
  43         switch(inpType) {
  44         case 's': in = samopen(inpF, "r", fn_list); break;
  45         case 'b': in = samopen(inpF, "rb", fn_list); break;
  46         default: assert(false);
  47         }
  48         assert(in != 0);
  49
  50         //build mappings from external sid to internal sid
  51         transcripts.buildMappings(in->header->n_targets, in->header->target_name);
  52
  53         //generate output's header
  54         bam_header_t *out_header = bam_header_dwt(in->header);
  55         for (int i = 0; i < out_header->n_targets; i++) {
  56                 out_header->target_len[i] = transcripts.getTranscriptViaEid(i + 1).getLength();  // transcript length without poly(A) tail
  57         }
  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         int cnt = 0;
  80
  81         b = bam_init1();
  82
  83         while (samread(in, b) >= 0) {
  84                 ++cnt;
  85                 if (verbose && cnt % 1000000 == 0) { printf("%d alignment lines are loaded!\n", cnt); }
  86
  87                 if (b->core.flag & 0x0004) continue;
  88
  89                 hit = wrapper.getNextHit();
  90                 assert(hit != NULL);
  91
  92                 assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
  93                 convert(b, hit->getConPrb());
  94                 if (b->core.qual > 0) samwrite(out, b); // output only when MAPQ > 0
  95         }
  96
  97         assert(wrapper.getNextHit() == NULL);
  98
  99         bam_destroy1(b);
 100         if (verbose) { printf("Bam output file is generated!\n"); }
 101 }
 102
 103 void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
 104         bam1_t *b, *b2;
 105         PairedEndHit *hit;
 106
 107         int cnt = 0;
 108
 109         b = bam_init1();
 110         b2 = bam_init1();
 111
 112         while (samread(in, b) >= 0 && samread(in, b2) >= 0) {
 113                 cnt += 2;
 114                 if (verbose && cnt % 1000000 == 0) { printf("%d alignment lines are loaded!\n", cnt); }
 115
 116                 if ((b->core.flag & 0x0004) || (b2->core.flag & 0x0004)) continue;
 117
 118                 //swap if b is mate 2
 119                 if (b->core.flag & 0x0080) {
 120                         assert(b2->core.flag & 0x0040);
 121                         bam1_t *tmp = b;
 122                         b = b2; b2 = tmp;
 123                 }
 124
 125                 hit = wrapper.getNextHit();
 126                 assert(hit != NULL);
 127
 128                 assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
 129                 assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
 130
 131                 convert(b, hit->getConPrb());
 132                 convert(b2, hit->getConPrb());
 133
 134                 b->core.mpos = b2->core.pos;
 135                 b2->core.mpos = b->core.pos;
 136
 137                 if (b->core.qual > 0) {
 138                         samwrite(out, b);
 139                         samwrite(out, b2);
 140                 }
 141         }
 142
 143         assert(wrapper.getNextHit() == NULL);
 144
 145         bam_destroy1(b);
 146         bam_destroy1(b2);
 147
 148         if (verbose) { printf("Bam output file is generated!\n"); }
 149 }
 150
 151 void BamWriter::convert(bam1_t *b, double prb) {
 152         const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);
 153
 154         int pos = b->core.pos;
 155         int readlen = b->core.l_qseq;
 156
 157         std::vector<uint32_t> data;
 158         data.clear();
 159
 160         int core_pos, core_n_cigar;
 161         std::vector<Interval> vec;
 162         vec.assign(1, Interval(1, transcript.getLength()));
 163         // make an artificial chromosome coordinates for the transcript to get new CIGAR strings
 164         tr2chr(Transcript("", "", "", '+', vec, ""), pos + 1, pos + readlen, core_pos, core_n_cigar, data);
 165         assert(core_pos >= 0);
 166
 167         int rest_len = b->data_len - b->core.l_qname - b->core.n_cigar * 4;
 168         b->data_len = b->core.l_qname + core_n_cigar * 4 + rest_len;
 169         expand_data_size(b);
 170         uint8_t* pt = b->data + b->core.l_qname;
 171         memmove(pt + core_n_cigar * 4, pt + b->core.n_cigar * 4, rest_len);
 172         for (int i = 0; i < core_n_cigar; i++) { memmove(pt, &data[i], 4); pt += 4; }
 173
 174         b->core.pos = core_pos;
 175         b->core.n_cigar = core_n_cigar;
 176         b->core.qual = getMAPQ(prb);
 177         b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&(b->core), bam1_cigar(b)));
 178
 179         float val = (float)prb;
 180         bam_aux_append(b, "ZW", 'f', bam_aux_type2size('f'), (uint8_t*)&val);
 181 }
 182
 183 #endif /* BAMWRITER_H_ */