cljam.io.sam
Functions to read and write the SAM (Sequence Alignment/Map) format and BAM (its binary equivalent). See https://samtools.github.io/hts-specs/ for the detail SAM/BAM specifications.
Functions to read and write the SAM (Sequence Alignment/Map) format and BAM (its binary equivalent). See https://samtools.github.io/hts-specs/ for the detail SAM/BAM specifications.
bam-readerclj
(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.
Returns an open cljam.io.bam.reader.BAMReader of f. Should be used inside with-open to ensure the reader is properly closed.
bam-writerclj
(bam-writer f)Returns an open cljam.io.bam.writer.BAMWriter of f. Should be used inside with-open to ensure the writer is properly closed.
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-readerclj
(clone-bam-reader r)Clones bam reader sharing persistent objects.
Clones bam reader sharing persistent objects.
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 alignments of the SAM/BAM file, returning the alignments as an eduction.
Reads alignments of the SAM/BAM file, returning the alignments as an eduction.
read-blocksclj
(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.
Reads alignment blocks of the SAM/BAM file, returning the blocks as an eduction.
read-headerclj
(read-header rdr)Returns header of the SAM/BAM file.
Returns header of the SAM/BAM file.
read-refsclj
(read-refs rdr)Returns references of the SAM/BAM file.
Returns references of the SAM/BAM file.
readerclj
(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.
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-readerclj
(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.
Returns an open cljam.io.sam.reader.SAMReader of f. Should be used inside with-open to ensure the reader is properly closed.
sam-writerclj
(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.
Returns an open cljam.io.sam.writer.SAMWriter of f. Should be used inside with-open to ensure the writer is properly closed.
write-alignmentsclj
(write-alignments wtr alignments header)Writes alignments to the SAM/BAM file.
Writes alignments to the SAM/BAM file.
write-blocksclj
(write-blocks wtr blocks)Writes alignment blocks of the SAM/BAM file.
Writes alignment blocks of the SAM/BAM file.
write-headerclj
(write-header wtr header)Writes header to the SAM/BAM file.
Writes header to the SAM/BAM file.
write-refsclj
(write-refs wtr header)Writes references to the SAM/BAM file.
Writes references to the SAM/BAM file.
writerclj
(writer f)Selects suitable writer from f's extension, returning the writer. This function supports SAM and BAM format.
Selects suitable writer from f's extension, returning the writer. This function supports SAM and BAM format.
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