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Viewing changes to src/org/usadellab/trimmomatic/Pairomatic.java

  • Committer: Package Import Robot
  • Author(s): Andreas Tille, Olivier Sallou
  • Date: 2013-08-07 12:14:33 UTC
  • mfrom: (1.1.1)
  • Revision ID: package-import@ubuntu.com-20130807121433-qxchmfrrodridtvz
Tags: 0.30+dfsg-1
http://bugs.debian.org/718850
* New upstream version
* debian/copyright:
   - DEP5
   - Add Files-Excluded to document what was removed from original source
* debian/watch: handle +dfsg suffix
* debian/get-orig-source: use new uscan if available
* debian/control:
   - cme fix dpkg-control
   - debhelper 9
   - use anonscm in Vcs fields
   - Build-Depends: default-jdk | ...
     Closes: #718850
[ Olivier Sallou]
    * Manage java libs with javahelper
    * Provide upstream missing MANIFEST.MF

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src/org/usadellab/trimmomatic/Pairomatic.java
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                        Character delimiter) throws IOException
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        {
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                Set<String> names1 = getFastqNames(input1, delimiter);
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                System.out.println("First input file contains " + names1.size() + " records");
 
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                System.err.println("First input file contains " + names1.size() + " records");
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                Set<String> names2 = getFastqNames(input2, delimiter);
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                System.out.println("Second input file contains " + names2.size() + " records");
 
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                System.err.println("Second input file contains " + names2.size() + " records");
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                names1.retainAll(names2);
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                System.out.println("Files shared " + names1.size() + " records");
 
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                System.err.println("Files shared " + names1.size() + " records");
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                names2.retainAll(names1);
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                if(!equalOrdering(names1,names2))
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                        {
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                        System.out.println("Error: Common records are not in identical order, cowardly refusing to do anything");
 
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                        System.err.println("Error: Common records are not in identical order, cowardly refusing to do anything");
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                        return;
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                        }
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                System.out.println("Splitting first file");
 
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                System.err.println("Splitting first file");
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                splitFastq(input1, output1P, output1U, names1, delimiter);
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                System.out.println("Splitting second file");
 
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                System.err.println("Splitting second file");
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                splitFastq(input2, output2P, output2U, names1, delimiter);
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                System.out.println("All done");
 
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                System.err.println("All done");
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        }
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        public static void main(String[] args) throws IOException
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                                String delimStr=args[argIndex++];
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                                if(delimStr.length()!=1)
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                                        System.out.println("Delimiter must be exactly one character, got '"+delimStr+"'");
 
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                                        System.err.println("Delimiter must be exactly one character, got '"+delimStr+"'");
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                                else
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                                        delim=delimStr.charAt(0);
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                                }
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                        else
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                                {
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                                System.out.println("Unknown option " + arg);
 
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                                System.err.println("Unknown option " + arg);
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                                badOption = true;
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                                }
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                        }
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                if (args.length - argIndex < 6 || badOption)
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                        {
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                        System.out
 
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                        System.err
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                                        .println("Usage: Pairomatic [-delim delimChar] <inputFile1> <inputFile2> <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>");
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                        System.exit(1);
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                        }