cljam.io.util

I/O utilities.

alignment-reader?

(alignment-reader? rdr)
Checks if given object implements protocol IAlignmentReader.

alignment-writer?

(alignment-writer? wtr)
Checks if given object implements protocol IAlignmentWriter.

bam-reader?

(bam-reader? rdr)
Checks if given object is an instance of BAMReader.

bam-writer?

(bam-writer? wtr)
Checks if given object is an instance of BAMWriter.

bcf-reader?

(bcf-reader? rdr)
Checks if given object is an instance of BCFReader.

bcf-writer?

(bcf-writer? wtr)
Checks if given object is an instance of BCFWriter.

bed-reader?

(bed-reader? rdr)
Checks if given object is an instance of BEDReader.

bed-writer?

(bed-writer? wtr)
Checks if given object is an instance of BEDWriter.

bigwig-reader?

(bigwig-reader? rdr)
Checks if given object is an instance of BIGWIGReader.

cram-reader?

(cram-reader? rdr)
Checks if given object is an instance of CRAMReader.

fasta-reader?

(fasta-reader? rdr)
Checks if given object is an instance of FASTAReader.

fasta-writer?

(fasta-writer? wtr)
Checks if given object is an instance of FASTAWriter.

fastq-reader?

(fastq-reader? rdr)
Checks if given object is an instance of FASTQReader.

fastq-writer?

(fastq-writer? wtr)
Checks if given object is an instance of FASTQWriter

file-type

(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.

file-type-from-bytes

(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.

file-type-from-contents

(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.

sam-reader?

(sam-reader? rdr)
Checks if given object is an instance of SAMReader.

sam-writer?

(sam-writer? wtr)
Checks if given object is an instance of SAMWriter.

sequence-reader?

(sequence-reader? rdr)
Checks if given object implements protocol ISequenceReader.

sequence-writer?

(sequence-writer? wtr)
Checks if given object implements protocol ISequenceWriter.

twobit-reader?

(twobit-reader? rdr)
Checks if given object is an instance of TwoBitReader.

twobit-writer?

(twobit-writer? wtr)
Checks if given object is an instance of TwoBitWriter.

variant-reader?

(variant-reader? rdr)
Checks if given object implements protocol IVariantReader.

variant-writer?

(variant-writer? wtr)
Checks if given object implements protocol IVariantWriter.

vcf-reader?

(vcf-reader? rdr)
Checks if given object is an instance of VCFReader.

vcf-writer?

(vcf-writer? wtr)
Checks if given object is an instance of VCFWriter.

wig-reader?

(wig-reader? rdr)
Checks if given object is an instance of WIGReader.

wig-writer?

(wig-writer? wtr)
Checks if given object is an instance of WIGWriter.