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, if available, as a string in place of the fasta sequence header. Default value: FALSE
--identifier-to-headern/anoWhen this switch is provided, ignore the sequence description line and write the sequence identifier, if available, as a string in place of the fasta sequence header. Default value: FALSE
--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. Default value: FALSE
--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. Default value: FALSE
--output-fake-qualityn/anoWhen this switch is provided, output fake qualities equal to fixed default constant quality. Default value: FALSE
--referencen/anoWhen this switch is provided with output-color-space, any transition on the N character will result in writing an ‘N’ base. Default value: FALSE
--trim-adaptor-lengthtrim-adaptor-lengthnoWhen positive, removes this many bases from the beginning of sequence. Default value: 0
(-n|--fasta-line-length)fasta-line-lengthnoThe number of bases to write per line. Default value: 60
(-i|--input)inputyesName of the compact input file.
(-o|--output)outputyesName of the fasta file output.
(-p|--pair-output)pair-outputnoName 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. Default value: fasta
(-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+ Default value: Illumina
(-s|--start-position)start-positionnoThe start position within the file, which should be number of bytes into the file to start reading from. The read will actually start at the first record on or after start-position.
(-e|--end-position)end-positionnoThe end position within the file, which should be number of bytes into the file to end reading from. The read will actually end at the end of the record on or after end-position.
-xdynamic-optionsnoSet a dynamic option, in the format classname:key=value. Classname is the the name of the class that exposes the option (short class name without package), key identifies the option to change and value is the new value for the option.