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Added option "append": if set, and the specified discovery output already exists, don't re-call anything that's already present in that file. Append new calls to it. 

Great for resuming long jobs that died partway through.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2219 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-12-02 18:56:19 +00:00
parent 0a2304eff8
commit c180a76b05
1 changed files with 55 additions and 11 deletions
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66
java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller2.java
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@ -39,6 +39,8 @@ public class MultiSampleCaller2 extends LocusWalker<MultiSampleCaller2.MultiSamp
@Argument(fullName="ALLELE_FREQ_TOLERANCE", shortName="AFT", required=false, doc="")
public double ALLELE_FREQ_TOLERANCE = 1e-6;
@Argument(fullName="append", shortName="append", required=false, doc="if the discovery file already exists, don't re-call sites that are done.") boolean APPEND = false;
private static final double MIN_LOD_FOR_STRAND = 0.01;
// Private state.
@ -183,17 +185,57 @@ public class MultiSampleCaller2 extends LocusWalker<MultiSampleCaller2.MultiSamp
}
}
private void maybeInitializeDisoveryOutput() {
if ( discovery_output_file == null ) {
try {
//final String filename = String.format("%s_%s_%d.calls", DISCOVERY_OUTPUT, loc.getContig(), loc.getStart());
final String filename = DISCOVERY_OUTPUT;
//System.out.printf("opening %s%n", filename);
discovery_output_file = new PrintStream(filename);
discovery_output_file.println(new MultiSampleCallResult().header());
} catch (Exception e) {
throw new RuntimeException(e);
}
GenomeLoc highest_previously_done_loc = null;
private boolean in_skip_mask(GenomeLoc loc)
{
if (highest_previously_done_loc == null) { return false; }
if (highest_previously_done_loc.compareTo(loc) < 0) { return false; }
else { return true; }
}
private void maybeInitializeDisoveryOutput()
{
if ( discovery_output_file == null )
{
File file = new File(DISCOVERY_OUTPUT);
if ((APPEND == true) && (file.exists()))
{
try
{
Runtime.getRuntime().exec("cp -v " + DISCOVERY_OUTPUT + " " + DISCOVERY_OUTPUT + ".backup");
// 1. Read the existing file and record the highest site we've seen.
Scanner scanner = new Scanner(file);
while(scanner.hasNext())
{
String line = scanner.nextLine();
String[] tokens = line.split(" +");
String loc_string = tokens[0];
if (loc_string.equals("loc")) { continue; }
highest_previously_done_loc = GenomeLocParser.parseGenomeLoc(loc_string);
}
// 2. Open the output file for appending.
discovery_output_file = new PrintStream(new FileOutputStream(DISCOVERY_OUTPUT, true));
}
catch (Exception e)
{
throw new RuntimeException(e);
}
}
else
{
try
{
final String filename = DISCOVERY_OUTPUT;
discovery_output_file = new PrintStream(filename);
discovery_output_file.println(new MultiSampleCallResult().header());
}
catch (Exception e)
{
throw new RuntimeException(e);
}
}
}
}
@ -266,6 +308,8 @@ public class MultiSampleCaller2 extends LocusWalker<MultiSampleCaller2.MultiSamp
{
if (start_time == null) { start_time = new Date(); }
if (in_skip_mask(context.getLocation()) == true) { return null; }
if ((n_sites_processed % 1000) == 0)
{
Date current_time = new Date();