Package 

Class CreateCSV_TrimmedAnchorLoading

  • All Implemented Interfaces:
    
public class CreateCSV_TrimmedAnchorLoading

    This method takes as input 2 csv files It takes the data from FindTrimmedAnchorCoordinates.jar, then calculates new coordinates using the old ref coordinates CSV file used for loading. The data is written to another csv file that will contain: chr,trimmedStart,trimmedEnd,GeneStart,GeneEnd The genes come from the old ref coordinates CSV file. Here are the caluclations for this method: Origial anchor 2: start/end: 50358-56716 = len 6358 Regex: start/end: 387-5359 = len 4972 New anchor 2: start = oldStart + regexStart = 50358+387 = 50745 end = start + regexLen -1 = 50745 + 4972 -1 = 55716 number trimmed at start = 387 number trimmed at end = oldEnd - newEnd = 56716-55716 = 1000 Output: Method creates the csv file needed for loading ref anchors to new trimmed DB.

    • Nested Class Summary

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    • Field Summary

      Fields 
      Modifier and Type Field Description

    • Constructor Summary

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      Constructor Description

    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description

    • Method Summary

      Modifier and Type Method Description
      static void processMain(String regexDataFile, String origRefAnchors, String outputFile)
      static void main(Array<String> args)

      • Methods inherited from class java.lang.Object

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