- alignment-reader?
- alignment-writer?
- bam-reader?
- bam-writer?
- bcf-reader?
- bcf-writer?
- bed-reader?
- bed-writer?
- bigwig-reader?
- fasta-reader?
- fasta-writer?
- fastq-reader?
- fastq-writer?
- file-type
- file-type-from-bytes
- file-type-from-contents
- sam-reader?
- sam-writer?
- sequence-reader?
- sequence-writer?
- twobit-reader?
- twobit-writer?
- variant-reader?
- variant-writer?
- vcf-reader?
- vcf-writer?
- wig-reader?
- wig-writer?
cljam.io.util
I/O utilities.
I/O utilities.
alignment-reader?clj
(alignment-reader? rdr)Checks if given object implements protocol IAlignmentReader.
Checks if given object implements protocol IAlignmentReader.
alignment-writer?clj
(alignment-writer? wtr)Checks if given object implements protocol IAlignmentWriter.
Checks if given object implements protocol IAlignmentWriter.
bam-reader?clj
(bam-reader? rdr)Checks if given object is an instance of BAMReader.
Checks if given object is an instance of BAMReader.
bam-writer?clj
(bam-writer? wtr)Checks if given object is an instance of BAMWriter.
Checks if given object is an instance of BAMWriter.
bcf-reader?clj
(bcf-reader? rdr)Checks if given object is an instance of BCFReader.
Checks if given object is an instance of BCFReader.
bcf-writer?clj
(bcf-writer? wtr)Checks if given object is an instance of BCFWriter.
Checks if given object is an instance of BCFWriter.
bed-reader?clj
(bed-reader? rdr)Checks if given object is an instance of BEDReader.
Checks if given object is an instance of BEDReader.
bed-writer?clj
(bed-writer? wtr)Checks if given object is an instance of BEDWriter.
Checks if given object is an instance of BEDWriter.
bigwig-reader?clj
(bigwig-reader? rdr)Checks if given object is an instance of BIGWIGReader.
Checks if given object is an instance of BIGWIGReader.
fasta-reader?clj
(fasta-reader? rdr)Checks if given object is an instance of FASTAReader.
Checks if given object is an instance of FASTAReader.
fasta-writer?clj
(fasta-writer? wtr)Checks if given object is an instance of FASTAWriter.
Checks if given object is an instance of FASTAWriter.
fastq-reader?clj
(fastq-reader? rdr)Checks if given object is an instance of FASTQReader.
Checks if given object is an instance of FASTQReader.
fastq-writer?clj
(fastq-writer? wtr)Checks if given object is an instance of FASTQWriter
Checks if given object is an instance of FASTQWriter
file-typeclj
(file-type f)Detects a file format from a path of f, returning a keyword representing the format. Throws an exception if an unsupported file is supplied.
Detects a file format from a path of f, returning a keyword representing the format. Throws an exception if an unsupported file is supplied.
file-type-from-bytesclj
(file-type-from-bytes ba)Tries to detect a file format based on contents of the byte array ba.
The input byte array must be larger than 4 bytes. Note that detection of some
formats #{:fasta :fastq :wig :fai :bed} is based on naive heuristics and
thus can fail.
Tries to detect a file format based on contents of the byte array `ba`.
The input byte array must be larger than 4 bytes. Note that detection of some
formats `#{:fasta :fastq :wig :fai :bed}` is based on naive heuristics and
thus can fail.file-type-from-contentsclj
(file-type-from-contents f)Detects a file format based on contents of the input file f. Causes a side
effect of reading some header bytes.
Detects a file format based on contents of the input file `f`. Causes a side effect of reading some header bytes.
sam-reader?clj
(sam-reader? rdr)Checks if given object is an instance of SAMReader.
Checks if given object is an instance of SAMReader.
sam-writer?clj
(sam-writer? wtr)Checks if given object is an instance of SAMWriter.
Checks if given object is an instance of SAMWriter.
sequence-reader?clj
(sequence-reader? rdr)Checks if given object implements protocol ISequenceReader.
Checks if given object implements protocol ISequenceReader.
sequence-writer?clj
(sequence-writer? wtr)Checks if given object implements protocol ISequenceWriter.
Checks if given object implements protocol ISequenceWriter.
twobit-reader?clj
(twobit-reader? rdr)Checks if given object is an instance of TwoBitReader.
Checks if given object is an instance of TwoBitReader.
twobit-writer?clj
(twobit-writer? wtr)Checks if given object is an instance of TwoBitWriter.
Checks if given object is an instance of TwoBitWriter.
variant-reader?clj
(variant-reader? rdr)Checks if given object implements protocol IVariantReader.
Checks if given object implements protocol IVariantReader.
variant-writer?clj
(variant-writer? wtr)Checks if given object implements protocol IVariantWriter.
Checks if given object implements protocol IVariantWriter.
vcf-reader?clj
(vcf-reader? rdr)Checks if given object is an instance of VCFReader.
Checks if given object is an instance of VCFReader.
vcf-writer?clj
(vcf-writer? wtr)Checks if given object is an instance of VCFWriter.
Checks if given object is an instance of VCFWriter.
wig-reader?clj
(wig-reader? rdr)Checks if given object is an instance of WIGReader.
Checks if given object is an instance of WIGReader.
wig-writer?clj
(wig-writer? wtr)Checks if given object is an instance of WIGWriter.
Checks if given object is an instance of WIGWriter.
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