htslib C API: getting reads from region
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5.8 years ago

I want to use the htslib C API to perform this task

 

my $pos = "1:100-1000";

my $bam_file = "in.bam";

my @reads = get_reads_from_htslib($bam_file,$pos)


foreach(@reads) {

    # do stuff...

}

 

I wrote it in perl but you get the idea. I can't find an example anywhere online. Does anyone have experience with htslib and getting reads from a region?

C API htslib samtools • 5.5k views
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5
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5.8 years ago

here is a C code:

 

compilation:

gcc -Isamtools -Ihtslib -Lsamtools -Lhtslib biostar151053.c htslib/libhts.a samtools/libbam.a -lz -lpthread
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Livesaver thanks!

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What function calls here come from samtools.h?

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may be none :-)

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Dear Pierre, I have another question. Now I have a sam file without the index file, and I want to iterate all the reads of the sam file, how can I make it? Thanks in advance.

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It seems that I have to compress the sam file to bam file, and get the index file then I can make it..

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Dear Pierre I used the exact code and bash line but I face an error. I've downloaded htslib and samtools and put them in the same folder as the .c file.

.... "_lzma_stream_decoder", referenced from: _cram_uncompress_block in libhts.a(cram_io.o) ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation)

Should I build samtools and htslib as mentioned here ?

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I think so, furthermore, the code above is ~5 years old, the htslib has since much changed.

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Thanks for fast respond.

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