Converting bam to sam using htslib C++ api

Question

[Uveyik]

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.

[Pierre Lindenbaum]

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Extract bam file to sam inside code?

GAM file columns?

Answer 1

[Pierre Lindenbaum]

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