89 lines
2.9 KiB
Java
89 lines
2.9 KiB
Java
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package edu.mit.broad.picard.util;
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import edu.mit.broad.picard.cmdline.CommandLineProgram;
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import edu.mit.broad.picard.cmdline.Usage;
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import edu.mit.broad.picard.cmdline.Option;
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import edu.mit.broad.picard.io.IoUtil;
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import java.io.File;
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import java.util.Date;
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import java.text.SimpleDateFormat;
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/**
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* CommandLineProgram to create Picard analysis directory
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*
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* @author Kathleen Tibbetts
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*/
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public class CreateAnalysisDirectory extends CommandLineProgram {
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public static final SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy_MM_dd");
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// The following attributes define the command-line arguments
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@Usage(programVersion="1.0")
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public String USAGE =
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"Usage: " + getClass().getName() + " [options]\n\n" +
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"Create a new Picard analysis directory.\n";
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@Option(shortName = "P", doc = "Analysis directory prefix. ")
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public String PREFIX = "/seq/picard";
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@Option(shortName = "F", doc = "The flowcell. ")
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public String FLOWCELL;
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@Option(shortName = "A", doc = "The first cycle being analyzed. ")
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public Integer FIRST_CYCLE = 1;
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@Option(shortName = "O", doc = "The last cycle being analyzed. ")
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public Integer LAST_CYCLE;
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@Option(shortName = "R", doc = "The run date in the format MM/dd/yyyy. ")
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public Date RUNDATE;
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@Option(shortName = "L", doc = "Lane number. ")
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public Integer LANE;
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@Option(shortName="LIB", doc = "Library this analysis is for (e.g. 'Solexa-1234'). ")
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public String LIBRARY;
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@Option(shortName="S", doc = "Analysis start date in the format MM/dd/yyyy")
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public Date ANALYSIS_START_DATE;
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@Override
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protected int doWork() {
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if (PREFIX.charAt(PREFIX.length()-1) == '/') {
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PREFIX = PREFIX.substring(0, PREFIX.length()-1);
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}
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IoUtil.assertDirectoryIsWritable(new File(PREFIX));
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String parts[] = { PREFIX, FLOWCELL, "C" + FIRST_CYCLE + "-" + LAST_CYCLE + "_" +
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dateFormat.format(RUNDATE) + "_" + dateFormat.format(ANALYSIS_START_DATE),
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String.valueOf(LANE), LIBRARY };
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String directory = null;
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for (int i = 1; i < parts.length; i++) {
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StringBuilder sb = new StringBuilder();
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for (int j=0; j <= i; j++) {
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sb.append(parts[j]).append("/");
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}
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directory = sb.toString();
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File dir = new File(directory);
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if (!dir.exists()) {
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if (!dir.mkdir()) {
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System.err.println("Unable to create directory " + directory);
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return 1;
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}
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}
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}
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System.out.print(directory);
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return 0;
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}
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public static void main(String[] argv) {
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CreateAnalysisDirectory cmd = new CreateAnalysisDirectory();
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cmd.QUIET = true;
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System.exit(cmd.instanceMain(argv));
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}
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}
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