Converters between equivalent formats: SAM/BAM and FASTA/TwoBit.
Converters between equivalent formats: SAM/BAM and FASTA/TwoBit.
(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.
(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.
(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.
(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.
(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.
(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.
(medium-qname aln)
Append _R1 or _R2 to the query name.
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.
Converts a SAM/BAM to a FASTQ file.
(short-qname aln)
Append /1 or /2 to the query name.
Append /1 or /2 to the query name.
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