cljam.algo.convert

Converters between equivalent formats: SAM/BAM and FASTA/TwoBit.

(aln->read {:keys [flag qual qname], seq' :seq})

Converts a SAM alignment record to a FASTQ read.

(convert in out & opts)

Converts file format from input file to output file by the file extension.

(convert-sam in out & {:keys [n-threads num-block create-index?], :or {n-threads 0, num-block default-num-block, create-index? false}})

Converts file format between SAM and BAM based on the file extension.

(convert-sequence in out)(convert-sequence xf in out)

Converts file format between FASTA and TwoBit based on the file extension.

(fq->seq in out)(fq->seq xf in out)

Converts a FASTQ file to a FASTA or TwoBit sequence file.

(long-qname aln)

Append casava 1.8 style R1/R2 suffix to the query name.

(medium-qname aln)

Append _R1 or _R2 to the query name.

(sam->fq xf in out)(sam->fq xf in out-r1 out-r2)(sam->fq xf in out-r0 out-r1 out-r2)

Converts a SAM/BAM to a FASTQ file.

(short-qname aln)

Append /1 or /2 to the query name.

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