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I was trying to extract the consensus seq from the particular part of remote BAM file. I was wondering whether it downloads total bam file or just the part of if which i needed (chr16:1000-1500)? First few lines of my code is given below.
Could you guys suggest me some docs/examples to understand Bio-Samtools better? (I am using this now http://search.cpan.org/~lds/Bio-SamTools-1.10/lib/Bio/DB/Sam.pm) |
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The perl module largely uses the C API using perl XS. Most functions, including use of an index to fetch subsets of this file, work identically to the C API. Unfortunately, the C API documentation is no more helpful than what you already have. As indicated in the perldoc you linked to on CPAN, when given a ftp or http URL, Bio::DB::Sam will retrieve the remote index, store it in the current working directory, and proceed to fetch just the subset of the file requested using http/ftp range operations. |
