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cljam.algo.convert

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

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

aln->readclj

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

Converts a SAM alignment record to a FASTQ read.

Converts a SAM alignment record to a FASTQ read.
sourceraw docstring

convertclj

(convert in out & opts)

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

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

convert-samclj

(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.

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

convert-sequenceclj

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

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

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

fq->seqclj

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

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

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

long-qnameclj

(long-qname aln)

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

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

medium-qnameclj

(medium-qname aln)

Append _R1 or _R2 to the query name.

Append _R1 or _R2 to the query name.
sourceraw docstring

sam->fqclj

(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.

Converts a SAM/BAM to a FASTQ file.
sourceraw docstring

short-qnameclj

(short-qname aln)

Append /1 or /2 to the query name.

Append /1 or /2 to the query name.
sourceraw docstring

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