Hey all,
I'd like to use samtools view function in my own code in order to map all the reads within some genomic coordinates such as chr1:200000-500000
There is main_samview function in sam_view.c source code file, however I couldn't figure it out how to use it in this case. Besides, when including sam_view.c in my program I get some compilation errors.
P.S. What I want to do is to store all the reads belong to a specific region in a vector of strings. I can view the reads in a region my using samtools view file.bam chr1:10000-50000, but I want to store them in a vector inside my program for later use.
Any help would be appreciated, thank you.
I'd like to use samtools view function in my own code in order to map all the reads within some genomic coordinates such as chr1:200000-500000
There is main_samview function in sam_view.c source code file, however I couldn't figure it out how to use it in this case. Besides, when including sam_view.c in my program I get some compilation errors.
P.S. What I want to do is to store all the reads belong to a specific region in a vector of strings. I can view the reads in a region my using samtools view file.bam chr1:10000-50000, but I want to store them in a vector inside my program for later use.
Any help would be appreciated, thank you.
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