org.monarchinitiative.vmvt.cli.commands.SequenceComparisonCommand

Direct Known Subclasses:: DeltaCommand, EseCommand, RulerCommand, TrekCommand, WalkerCommand

public class SequenceComparisonCommand
extends Object

Field Summary

Method Summary

Modifier and Type	Method	Description
`protected void`	`initSequences()`	Users are allowed t pass both sequences on the command line or to pass the path to a file that contains ref on the first line and alt on the second line.
`protected void`	`readInputFile()`

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- outname
  
  protected String outname
- reference
  
  protected String reference
- alternate
  
  protected String alternate
- infile
  
  protected String infile
- seqlen
  
  protected int seqlen
  
  Length of the sequences. Must be either 9 (donor) or 27 (acceptor)
Constructor Details
- SequenceComparisonCommand
  
  public SequenceComparisonCommand()
Method Details
- initSequences
  
  protected void initSequences()
  
  Users are allowed t pass both sequences on the command line or to pass the path to a file that contains ref on the first line and alt on the second line. This function checks if the user has p[assed the -i/--in flag and if so it reads the sequences from the file. If not, it checks that the user passed both the -r/--ref and -a/--alt flags. If there is an error, the function exits with an error message.
- readInputFile
  
  protected void readInputFile()