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Alpha - subject to change. Provides functions for reading from a CRAM file.
| (ns cljam.io.cram
(:refer-clojure :exclude [indexed?])
(:require [cljam.io.cram.core :as cram]
[cljam.io.protocols :as protocols]
[cljam.io.util :as io-util])
(:import [cljam.io.cram.reader CRAMReader]))
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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.
| (defn reader
(^CRAMReader [f] (reader f {}))
(^CRAMReader [f option]
(if (io-util/cram-reader? f)
(cram/clone-reader f)
(cram/reader f option))))
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Returns the header of the CRAM file.
| (defn read-header
[rdr]
(protocols/read-header rdr))
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Returns the references of the CRAM file.
| (defn read-refs
[rdr]
(protocols/read-refs rdr))
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Reads all the alignments from the CRAM file and returns them as a lazy sequence
of record maps.
| (defn read-alignments
([rdr]
(protocols/read-alignments rdr))
([rdr region]
(protocols/read-alignments rdr region)))
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Returns true if the reader can be randomly accessed, false if not. Note this
function immediately realizes a delayed index.
| (defn indexed?
[rdr]
(protocols/indexed? rdr))
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