cljam.io.cram
Alpha - subject to change. Provides functions for reading from a CRAM file.
Alpha - subject to change. Provides functions for reading from a CRAM file.
indexed?clj
(indexed? rdr)Returns true if the reader can be randomly accessed, false if not. Note this function immediately realizes a delayed index.
Returns true if the reader can be randomly accessed, false if not. Note this function immediately realizes a delayed index.
read-alignmentsclj
(read-alignments rdr)(read-alignments rdr region)Reads all the alignments from the CRAM file and returns them as a lazy sequence of record maps.
Reads all the alignments from the CRAM file and returns them as a lazy sequence of record maps.
read-headerclj
(read-header rdr)Returns the header of the CRAM file.
Returns the header of the CRAM file.
read-refsclj
(read-refs rdr)Returns the references of the CRAM file.
Returns the references of the CRAM file.
readerclj
(reader f)(reader f option)Creates a CRAM reader depending on the argument f: If f is a file or a string that representing the path to a CRAM file, returns a new reader that reads that CRAM file. If f is a CRAM reader, creates and returns a cloned CRAM reader from it.
The function also takes an optional argument option, which is a map that
consists of:
- reference: A string representing the path to the reference file, or a sequence reader that reads sequences from the reference file. This may be omitted only when the CRAM file to be read does not require a reference file.
Creates a CRAM reader depending on the argument f: If f is a file or a string
that representing the path to a CRAM file, returns a new reader that reads
that CRAM file. If f is a CRAM reader, creates and returns a cloned CRAM reader
from it.
The function also takes an optional argument `option`, which is a map that
consists of:
- reference: A string representing the path to the reference file, or
a sequence reader that reads sequences from the reference file.
This may be omitted only when the CRAM file to be read does not
require a reference file.cljdoc is a website building & hosting documentation for Clojure/Script libraries
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