Package 

Class FindTrimmedAnchorCoordinates

  • All Implemented Interfaces:
    
public class FindTrimmedAnchorCoordinates

    NOTE: This version works on the REF only. The assemblies do not have their coordinates in the fasta files - they only have the start, not the end. OH - but I could get it from the length. Due to time, I'm not going to mess this one up. I"ll write another one for assemblies and merge them later. Method takes - a refAnchor fasta file, (I dumped reference anchors from the pre-trimmed db) - a list of files from a directory that contain the trimmed versions on a per-anchor basis. Find the start and end of the trimmed sequence in the ref sequence. The start is where it matches. The end is the length of the trimmed sequence added to the start. Output: The important output is the csv file that will be used to load the new reference anchors to the "trimmed" database.

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description

    • Field Summary

      Fields 
      Modifier and Type Field Description

    • Constructor Summary

      Constructors 
      Constructor Description

    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description

    • Method Summary

      Modifier and Type Method Description
      static void processMain(String refFasta, Map<Integer, String> trimmedFastas, String outputDir, String lineName)
      static void main(Array<String> args)

      • Methods inherited from class java.lang.Object

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