Package net.sf.picard.reference

Examples of net.sf.picard.reference.IndexedFastaSequenceFile

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  }

  public static IndexedFastaSequenceFile createIndexedFastaSequenceFile(
      File file) throws RuntimeException, FileNotFoundException {
    if (IndexedFastaSequenceFile.canCreateIndexedFastaReader(file)) {
      IndexedFastaSequenceFile ifsFile = new IndexedFastaSequenceFile(
          file);

      return ifsFile;
    } else
      throw new RuntimeException(
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        String pathToBamFile = commandLine.getOptionValue("i");
        SAMFileReader reader = new SAMFileReader(new File(pathToBamFile));

        // Init reference
        String  pathToRef = commandLine.getOptionValue("r");
        IndexedFastaSequenceFile refIndex = new IndexedFastaSequenceFile(new File(pathToRef));

        int numberOfProblematicReads = 0;
        int numReads = 0;
        SAMRecordIterator iter = reader.iterator();
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