cljam.algo.depth
Provides algorithms for calculating simple depth of coverage.
Provides algorithms for calculating simple depth of coverage.
depthclj
(depth bam-reader
{:keys [chr start end] :or {start 1 end Long/MAX_VALUE}}
&
[{:keys [step unchecked? n-threads]
:or {step default-step unchecked? false n-threads 1}}])Calculate depth of coverage eagerly. Returns a seq of depth for range [start, end].
Requires a cljam.io.bam.reader.BAMReader instance and region.
If start and end are not supplied, piles whole range up.
Note that CIGAR code in alignments are ignored and only start/end positions are used.
Calculate depth of coverage eagerly. Returns a seq of depth for range [start, end]. Requires a `cljam.io.bam.reader.BAMReader` instance and region. If start and end are not supplied, piles whole range up. Note that CIGAR code in alignments are ignored and only start/end positions are used.
depth*clj
(depth* rdr
{:keys [chr start end] :as region}
&
[{:keys [step unchecked? n-threads]
:or {step default-step unchecked? false n-threads 1}}])Internal depth function which returns an int-array.
Internal depth function which returns an int-array.
lazy-depthclj
(lazy-depth bam-reader
{:keys [chr start end] :or {start 1 end Long/MAX_VALUE}}
&
[{:keys [step n-threads] :or {step default-step n-threads 1}}])Calculate depth of coverage lazily. Returns a lazy seq of depth for range [start, end].
Requires a cljam.io.bam.reader.BAMReader instance and region.
If start and end are not supplied, piles whole range up.
Note that CIGAR code in alignments are ignored and only start/end positions are used.
Calculate depth of coverage lazily. Returns a lazy seq of depth for range [start, end]. Requires a `cljam.io.bam.reader.BAMReader` instance and region. If start and end are not supplied, piles whole range up. Note that CIGAR code in alignments are ignored and only start/end positions are used.
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