I'm using the Pysam module of Python and calling the function:
VF = VariantFile("input_file") VF.fetch()
seems to retrieve all reads in the file,
while this retrieves reads from positions 0 to 1000 in one specific contig:
VF.fetch(contig="contig_name", start=0, end=1000)
My question is: is it possible to retrieve sequences based on positions without specifying the contig name? Or better, specifying multiple contig names? (gives error, expects one string).
This is because I have a file with multiple contigs, but I would like to get for example all reads in positions 0:1000 in all contigs.
If I do this:
VF.fetch( start=0, end=1000)
It ignores my start and end specification, and retrieves all reads, like if it were no arguments inside fetch.