cljam.io.sam
bam-reader
(bam-reader f)
Returns an open cljam.io.bam.reader.BAMReader of f. Should be used inside
with-open to ensure the reader is properly closed.
bam-writer
(bam-writer f)(bam-writer f create-index?)
Returns an open cljam.io.bam.writer.BAMWriter of f. Should be used inside
with-open to ensure the writer is properly closed.
clone-bam-reader
(clone-bam-reader r)
Clones bam reader sharing persistent objects.
indexed?
(indexed? rdr)
Returns true if the reader can be randomly accessed, false if not. Note this
function immediately realizes a delayed index.
read-alignments
(read-alignments rdr)(read-alignments rdr region)
Reads alignments of the SAM/BAM file, returning the alignments as an eduction.
read-blocks
(read-blocks rdr)(read-blocks rdr region)(read-blocks rdr region option)
Reads alignment blocks of the SAM/BAM file, returning the blocks as an eduction.
read-refs
(read-refs rdr)
Returns references of the SAM/BAM file.
reader
(reader f)
Selects suitable reader from f's extension, returning the reader. Opens a new
reader if the arg represents a file such as String path, java.io.File, or
java.net.URL. If a reader is given, clones the reader. This function supports
SAM and BAM formats.
sam-reader
(sam-reader f)
Returns an open cljam.io.sam.reader.SAMReader of f. Should be used inside
with-open to ensure the reader is properly closed.
sam-writer
(sam-writer f)
Returns an open cljam.io.sam.writer.SAMWriter of f. Should be used inside
with-open to ensure the writer is properly closed.
write-alignments
(write-alignments wtr alignments header)
Writes alignments to the SAM/BAM file.
write-blocks
(write-blocks wtr blocks)
Writes alignment blocks of the SAM/BAM file.
write-refs
(write-refs wtr header)
Writes references to the SAM/BAM file.
writer
(writer f)(writer f create-index?)
Selects suitable writer from f's extension, returning the writer. This
function supports SAM and BAM format.