public static void main(String[] args) { try { String inFile = "/psychipc01/disk2/references/1000Genome/release/20130502_v5a/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz"; String outFile = "/psychipc01/disk2/references/1000Genome/release/20130502_v5a/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes1.vcf.gz"; BlockCompressedInputStream br = new BlockCompressedInputStream(new File(inFile)); BlockCompressedOutputStream bw = new BlockCompressedOutputStream(new File(outFile)); String line = null; String[] cells = null; int[] orgIndices = new int[] { 0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 33, 34, 35, 36, 37, 38, 39, 40 }; int selectedColNum = orgIndices.length; int i, pos; String delimiter = "\t"; while ((line = br.readLine()) != null) { line = line.trim(); if (line.trim().length() == 0) { continue; } bw.write(line.replaceAll("[|]", "/").getBytes()); bw.write("\n".getBytes()); } bw.close(); br.close(); } catch (Exception ex) { ex.printStackTrace(); } }
@Override public void close() throws IOException { bci.close(); }