clj-biosequence.fastq — clj-biosequence 0.5.2

->fastqFile clj

(->fastqFile file opts)

Positional factory function for class clj_biosequence.fastq.fastqFile.

->fastqReader clj

(->fastqReader strm)

Positional factory function for class clj_biosequence.fastq.fastqReader.

->fastqSequence clj

(->fastqSequence description sequence quality)

Positional factory function for class clj_biosequence.fastq.fastqSequence.

->fastqString clj

(->fastqString str)

Positional factory function for class clj_biosequence.fastq.fastqString.

fastq->string clj

(fastq->string bs)

Returns a fastq sequence string.

init-fastq-file clj

(init-fastq-file path & opts)

Returns a fastqFile record.

init-fastq-sequence clj

(init-fastq-sequence description sequence quality)

Returns a fastq sequence record.

init-fastq-string clj

(init-fastq-string str)

Returns a fastqString record.

map->fastqFile clj

(map->fastqFile m__7585__auto__)

Factory function for class clj_biosequence.fastq.fastqFile, taking a map of keywords to field values.

map->fastqReader clj

(map->fastqReader m__7585__auto__)

Factory function for class clj_biosequence.fastq.fastqReader, taking a map of keywords to field values.

map->fastqSequence clj

(map->fastqSequence m__7585__auto__)

Factory function for class clj_biosequence.fastq.fastqSequence, taking a map of keywords to field values.

map->fastqString clj

(map->fastqString m__7585__auto__)

Factory function for class clj_biosequence.fastq.fastqString, taking a map of keywords to field values.

qualities clj

(qualities this)

Returns the quality string from a fastq sequence record.

shuffle-fq clj

(shuffle-fq forward reverse out)

Takes forward and reverse reads from paired end sequencing data and interleaves them in a single file.

unshuffle-fq clj

(unshuffle-fq forward-out reverse-out in)

Takes a fastq file with interleaved paired-end sequences and separates forward and reverse reads into separate files.