Question

Converting bam to sam using htslib C++ api

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4 weeks ago

Uveyik ▴ 40

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 • 262 views

ADD COMMENT • link updated 4 weeks ago by Pierre Lindenbaum 164k • written 4 weeks ago by Uveyik ▴ 40

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Extract bam file to sam inside code?

GAM file columns?

ADD REPLY • link 4 weeks ago by Pierre Lindenbaum 164k

score 2 · Answer 1 · 2024-09-29

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