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#ifndef BAMWRITER_H_
#define BAMWRITER_H_
#include<cmath>
#include<cstdio>
#include<cstring>
#include<cassert>
#include<string>
#include<sstream>
#include<iostream>
#include <stdint.h>
#include "htslib/sam.h"
#include "sam_utils.h"
#include "SamHeader.hpp"
#include "utils.h"
#include "my_assert.h"
#include "SingleHit.h"
#include "PairedEndHit.h"
#include "HitWrapper.h"
#include "Transcript.h"
#include "Transcripts.h"
class BamWriter {
public:
BamWriter(const char* inpF, const char* aux, const char* outF, Transcripts& transcripts, int nThreads);
~BamWriter();
void work(HitWrapper<SingleHit> wrapper);
void work(HitWrapper<PairedEndHit> wrapper);
private:
samFile *in, *out;
bam_hdr_t *in_header, *out_header;
Transcripts& transcripts;
void set_alignment_weight(bam1_t *b, double prb) {
b->core.qual = bam_prb_to_mapq(prb);
float val = (float)prb;
uint8_t *p = bam_aux_get(b, "ZW");
if (p != NULL) {
memcpy(p + 1, (uint8_t*)&(val), bam_aux_type2size('f'));
} else {
bam_aux_append(b, "ZW", 'f', bam_aux_type2size('f'), (uint8_t*)&val);
}
}
};
//aux can be NULL
BamWriter::BamWriter(const char* inpF, const char* aux, const char* outF, Transcripts& transcripts, int nThreads) : transcripts(transcripts) {
in = sam_open(inpF, "r");
assert(in != 0);
if (aux == NULL) hts_set_fai_filename(in, aux);
in_header = sam_hdr_read(in);
assert(in_header != 0);
//build mappings from external sid to internal sid
transcripts.buildMappings(in_header->n_targets, in_header->target_name);
//generate output's header
SamHeader hdr(in_header->text);
hdr.insertPG("RSEM");
out_header = hdr.create_header();
out = sam_open(outF, "wb"); // If CRAM format is desired, use "wc"
assert(out != 0);
sam_hdr_write(out, out_header);
if (nThreads > 1) general_assert(hts_set_threads(out, nThreads) == 0, "Fail to create threads for writing the BAM file!");
}
BamWriter::~BamWriter() {
bam_hdr_destroy(in_header);
sam_close(in);
bam_hdr_destroy(out_header);
sam_close(out);
}
void BamWriter::work(HitWrapper<SingleHit> wrapper) {
bam1_t *b;
SingleHit *hit;
HIT_INT_TYPE cnt = 0;
b = bam_init1();
while (sam_read1(in, in_header, b) >= 0) {
++cnt;
if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< " alignment lines are loaded!"<< std::endl; }
if (bam_is_mapped(b)) {
hit = wrapper.getNextHit();
assert(hit != NULL);
assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
set_alignment_weight(b, hit->getConPrb());
}
sam_write1(out, out_header, b);
}
assert(wrapper.getNextHit() == NULL);
bam_destroy1(b);
if (verbose) { std::cout<< "Bam output file is generated!"<< std::endl; }
}
void BamWriter::work(HitWrapper<PairedEndHit> wrapper) {
bam1_t *b, *b2;
PairedEndHit *hit;
HIT_INT_TYPE cnt = 0;
b = bam_init1();
b2 = bam_init1();
while (sam_read1(in, in_header, b) >= 0 && sam_read1(in, in_header, b2) >= 0) {
cnt += 2;
if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< " alignment lines are loaded!"<< std::endl; }
if (!bam_is_read1(b)) { bam1_t * tmp = b; b = b2; b2 = tmp; }
if (bam_is_mapped(b) && bam_is_mapped(b2)) {
hit = wrapper.getNextHit();
assert(hit != NULL);
assert(transcripts.getInternalSid(b->core.tid + 1) == hit->getSid());
assert(transcripts.getInternalSid(b2->core.tid + 1) == hit->getSid());
set_alignment_weight(b, hit->getConPrb());
set_alignment_weight(b2, hit->getConPrb());
}
sam_write1(out, out_header, b);
sam_write1(out, out_header, b2);
}
assert(wrapper.getNextHit() == NULL);
bam_destroy1(b);
bam_destroy1(b2);
if (verbose) { std::cout<< "Bam output file is generated!"<< std::endl; }
}
#endif /* BAMWRITER_H_ */
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