This mode is used to convert a compact file to FASTA format. It is implemented by edu.cornell.med.icb.goby.modes.CompactToFastaMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
--index-to-headern/anoWhen this switch is provided, ignore the sequence description line and write the sequence index as a string in place of the fasta sequence header.
--output-color-spacen/anoWhen this switch is provided, convert the sequence to color mode. Only makes sense if the compact file encodes a sequence in fasta format.
--output-fake-ntn/anoWhen this switch is provided, convert the color space sequence to fake nucleotide representation (e.g. 0123.->ACTGN). Used by the BWA algorithm.
--output-fake-qualityn/anoWhen this switch is provided, output fake qualities equal to fixed default constant quality.
--referencen/anoWhen this switch is provided with output-color-space, any transition on the N character will result in writing an ‘N’ base.
--trim-adaptor-lengthtrim-adaptor-lengthnoWhen positive, removes this many bases from the beginning of sequence.
(-i|--input)inputyesName of the compact input file.
(-o|--output)outputyesName of the fasta file output.
(-p|--pair-output)pair-outputyesName of the pair output file (where paired sequence will be written).
(-t|--output-format)output-formatnoType of output to generate. Can be Fasta or Fastq. The fastq format encodes quality scores.
(-a|--alphabet)alphabetnoAlphabet of valid bases/residues. The sequence is filtered to keep only characters in the alphabet. Other characters are replaced by ‘N’.
(-f|--read-index-filter)read-index-filternoThe name of a read index filter. When provided, compact-to-fasta will only write reads to the output if their index is contained in the filter.
--quality-encodingquality-encodingnoThe encoding for quality scores. The default quality encoding is that used by the Illumina pipeline 1.3+