Changeset 5


Ignore:
Timestamp:
Jun 26, 2012, 11:37:57 AM (7 years ago)
Author:
w.spee@…
Message:

changed the command line client to not take the test files but the actual command line parameters

File:
1 edited

Legend:

Unmodified
Added
Removed
  • XSQConverterJava/src/xsqconverterjava2/XSQConverterJava.java

    r3 r5  
    6161       
    6262       
    63 //        if(!requiredOptionsAreSet(cmd))
    64 //        {
    65 //            printHelp(options);           
    66 //        }       
    67 //       
    68 //        String xsqFilePath = cmd.getOptionValue("i");
    69 //        String outputPath = cmd.getOptionValue("o");
    70 //        long chunkSize =  new Long(cmd.getOptionValue("c", "1000000"));   
    71 //       
    72        
    73        
    74        
    75        
    76        
    77         String xsqFilePath = "/home/wim/Analysis/xsq_conversion_test/HU02_20120518_MixedRunRNA4CChIP_Nico_05.xsq";
    78         String outputPath = "/home/wim/Analysis/xsq_conversion_test/HU02_output6";
    79         long chunkSize =  new Long(1000000000);
     63        if(!requiredOptionsAreSet(cmd))
     64        {
     65            printHelp(options);           
     66        }       
     67       
     68        String xsqFilePath = cmd.getOptionValue("i");
     69        String outputPath = cmd.getOptionValue("o");
     70        long chunkSize =  new Long(cmd.getOptionValue("c", "1000000"));   
     71//       
     72       
     73       
     74       
     75       
     76       
     77//        String xsqFilePath = "/home/wim/Analysis/xsq_conversion_test/HU02_20120518_MixedRunRNA4CChIP_Nico_05.xsq";
     78//        String outputPath = "/home/wim/Analysis/xsq_conversion_test/HU02_output6";
     79//        long chunkSize =  new Long(1000000000);
    8080       
    8181        Map<String, String> librariesSubSet = new HashMap<String, String>();
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