cljam.io.protocols
Protocols of reader/writer for various file formats.
Protocols of reader/writer for various file formats.
IAlignmentReadercljprotocol
read-alignmentsclj
(read-alignments this)(read-alignments this 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 this)(read-blocks this region)(read-blocks this 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 this)Returns header of the SAM/BAM file.
Returns header of the SAM/BAM file.
read-refsclj
(read-refs this)Returns references of the SAM/BAM file.
Returns references of the SAM/BAM file.
IAlignmentWritercljprotocol
write-alignmentsclj
(write-alignments this alignments header)Writes alignments to the SAM/BAM file.
Writes alignments to the SAM/BAM file.
write-blocksclj
(write-blocks this blocks)Writes alignment blocks of the SAM/BAM file.
Writes alignment blocks of the SAM/BAM file.
write-headerclj
(write-header this header)Writes header to the SAM/BAM file.
Writes header to the SAM/BAM file.
write-refsclj
(write-refs this header)Writes references to the SAM/BAM file.
Writes references to the SAM/BAM file.
IReadercljprotocol
indexed?clj
(indexed? this)Returns true if the reader can be randomly accessed, false if not.
Returns true if the reader can be randomly accessed, false if not.
readclj
(read this)(read this option)Sequentially reads contents of the file.
Sequentially reads contents of the file.
reader-urlclj
(reader-url this)Returns the file's URL.
Returns the file's URL.
IRegionReadercljprotocol
read-in-regionclj
(read-in-region this region)(read-in-region this region option)Reads contents of the file in given region.
Reads contents of the file in given region.
ISequenceReadercljprotocol
read-all-sequencesclj
(read-all-sequences this)(read-all-sequences this option)Reads all sequences of FASTA/2BIT file.
Reads all sequences of FASTA/2BIT file.
read-indicesclj
(read-indices this)Reads metadata of indexed sequences in FASTA/2BIT file.
Reads metadata of indexed sequences in FASTA/2BIT file.
read-seq-summariesclj
(read-seq-summaries this)Reads summaries of sequences in the file.
Reads summaries of sequences in the file.
read-sequenceclj
(read-sequence this region)(read-sequence this region option)Reads sequence in region of FASTA/2BIT file.
Reads sequence in region of FASTA/2BIT file.
ISequenceWritercljprotocol
write-sequencesclj
(write-sequences this seqs)Writes all sequences to FASTA/2BIT file.
Writes all sequences to FASTA/2BIT file.
IVariantReadercljprotocol
headerclj
(header this)Returns header of VCF/BCF file as a sequence of strings.
Returns header of VCF/BCF file as a sequence of strings.
meta-infoclj
(meta-info this)Returns meta-info section of VCF/BCF file as a map.
Returns meta-info section of VCF/BCF file as a map.
read-file-offsetsclj
(read-file-offsets rdr)Reads file-offsets of VCF/BCF file
Reads file-offsets of VCF/BCF file
read-variantsclj
(read-variants this)(read-variants this option)Reads variants of the VCF/BCF file, returning them as a lazy sequence.
Reads variants of the VCF/BCF file, returning them as a lazy sequence.
read-variants-randomlyclj
(read-variants-randomly this region-option depth-option)Reads randomly variants of the VCF/BCF file, returning them as a lazy sequence.
Reads randomly variants of the VCF/BCF file, returning them as a lazy sequence.
IVariantWritercljprotocol
write-variantsclj
(write-variants this variants)Writes variants to thee VCF/BCF file.
Writes variants to thee VCF/BCF file.
IWritercljprotocol
writer-urlclj
(writer-url this)Returns the source's URL.
Returns the source's URL.
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