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cljam.io.bam-index.core
The core of BAM index features.
The core of BAM index features.
bam-indexclj
(bam-index f)Reads the given BAI file f and returns its contents as a cljam.bam-index.core.BAMIndex.
Reads the given BAI file `f` and returns its contents as a `cljam.bam-index.core.BAMIndex`.
bin-indexclj
(bin-index f ref-idx)Returns binning index for the given reference index.
Returns binning index for the given reference index.
create-indexclj
(create-index f alns refs)Creates a BAM index file from the alignments and references data.
Creates a BAM index file from the alignments and references data.
get-spansclj
(get-spans bai ref-idx beg end)Returns regions of a BAM file that may contain an alignment for the given range.
Returns regions of a BAM file that may contain an alignment for the given range.
get-unplaced-spansclj
(get-unplaced-spans bai)Returns a sequence of [start end) pairs of virtual file offsets that may contain alignments that don't have RNAME.
Returns a sequence of [start end) pairs of virtual file offsets that may contain alignments that don't have RNAME.
linear-indexclj
(linear-index f ref-idx)Returns linear index for the given reference index.
Returns linear index for the given reference index.
writerclj
(writer f refs)Returns an open cljam.io.bam_index.writer.BAIWriter of f. Should be used inside with-open
to ensure the writer is properly closed.
Returns an open `cljam.io.bam_index.writer.BAIWriter` of `f`. Should be used inside with-open to ensure the writer is properly closed.
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