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Support for indexed fasta files as reference sequences #495
Addressing issue #317
This could be implemented may different ways, I just made it so that the fasta file and index (<fasta_file>.fai) end up in the seq directory, and the fai is used to determine the offsets for loading the sequence.
There is no explicit chunk size, but this uses XHRBlob which downloads in 64kb chunks.
There is no support for compressed fasta files. This would be doable-- it would require additional preparation-- specifically bgzipping the fasta file and making a file which contains offsets to bgzf blocks.
That particular part of the git branch may not be necessary, and I probably
So removing query.seqChunkSize isn't necessary for using IndexedFasta as
On Thu, Jul 17, 2014 at 9:18 PM, Colin email@example.com wrote:
Yes I wasn't sure myself if it is unused or not. Thanks for checking that
On Thu, Jul 17, 2014 at 8:47 PM, Bradford Powell firstname.lastname@example.org
How likely is it that compressed fasta will be supported? The latter samtools packages provide the tools to compress the reference and this could be presented to
Should #317 still be open?