C++使用htslib库读入和写出bam文件的实例

2020-05-23 13:37:05

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有时候我们需要使用C++处理bam文件，比如取出read1或者read2等符合特定条件的序列，根据cigar值对序列指定位置的碱基进行统计或者对序列进行处理并输出等，这时我们可以使用htslib库。htslib可以用来处理SAM, BAM,CRAM 和VCF文件，是samtools、bcftools的核心库。

#include <stdio.h>#include <stdlib.h>#include <htslib/sam.h>using namespace std; #define bam_is_read1(b) (((b)->core.flag&BAM_FREAD1) != 0)uint8_t Base[16] = {0,65,67,0,71,0,0,0,84,0,0,0,0,0,0,78};int main(int argc, char **argv){ bam_hdr_t *header; bam1_t *aln = bam_init1(); samFile *in = sam_open(argv[1], "r"); htsFile *outR1 = hts_open(argv[2], "wb"); header = sam_hdr_read(in); if (sam_hdr_write(outR1, header) < 0) { fprintf(stderr, "Error writing output./n"); exit(-1); } uint8_t *seq; int32_t lseq; uint32_t *cigar; char* qname; while (sam_read1(in, header, aln) >= 0) { if (bam_is_read1(aln)){  sam_write1(outR1, header, aln); } else {  seq = bam_get_seq(aln);  lseq = aln->core.l_qseq;  qname = bam_get_qname(aln);  printf("%s/n",qname);  cigar = bam_get_cigar(aln);  for(int i=0; i < aln->core.n_cigar;++i){  int icigar = cigar[i];  printf("%d%d/n",bam_cigar_op(icigar),bam_cigar_oplen(icigar));  }  for(int i=0; i < lseq;++i){  printf("%c", Base[bam_seqi(seq, i)]);  }  printf("/n"); } } sam_close(in); sam_close(outR1);}

cigar值存储形式

32位int，通过bam_get_cigar获得地址，aln->core.n_cigar返回cigar operation的个数

•低 4位存储cigar operation；通过函数bam_cigar_op()获得operation

htslib库,读入,写出,bam文件,C++