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Converting bam to sam using htslib C++ api

Hi everyone, is it possible to convert between sam and bam file inside C++ code. I knowhtslib library offers implementation of file formats including sam and bam. However, I could not find a documentation describing this conversion. I know samtools view command can be used for this purpose but I need to deal with this inside C++ code.

bam htslib sam
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Uveyik • Uveyik

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Extract bam file to sam inside code?

GAM file columns?

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

read https://github.com/samtools/samtools/blob/develop/sam_view.c

  • allocate a new bam1_t* b = bam_init1
  • open the input file: sam_open_format
  • read the header sam_hdr_read
  • open the output file: sam_open_format
  • write the header: sam_hdr_str
  • while you can read a bam1_t : sam_read1
  • write the read sam_format1
  • dispose header sam_hdr_destroy
  • dispose read bam_destroy1
  • dispose files: sam_close
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written by Pierre Lindenbaum Pierre Lindenbaum

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