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GSA-491: Add hidden tag to GATK that propagates to the GATK logs

This commit is contained in:
Mark DePristo 2012-08-20 13:19:35 -04:00
parent 9eec33ec3b
commit 6ce8016ae7
2 changed files with 28 additions and 0 deletions
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23
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -64,12 +64,35 @@ public class GATKArgumentCollection {
@Argument(fullName = "read_buffer_size", shortName = "rbs", doc="Number of reads per SAM file to buffer in memory", required = false)
public Integer readBufferSize = null;
// --------------------------------------------------------------------------------------------------------------
//
// GATKRunReport options
//
// --------------------------------------------------------------------------------------------------------------
@Argument(fullName = "phone_home", shortName = "et", doc="What kind of GATK run report should we generate? STANDARD is the default, can be NO_ET so nothing is posted to the run repository. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false)
public GATKRunReport.PhoneHomeOption phoneHomeType = GATKRunReport.PhoneHomeOption.STANDARD;
@Argument(fullName = "gatk_key", shortName = "K", doc="GATK Key file. Required if running with -et NO_ET. Please see " + GATKRunReport.PHONE_HOME_DOCS_URL + " for details.", required = false)
public File gatkKeyFile = null;
/**
* The GATKRunReport supports (as of GATK 2.2) tagging GATK runs with an arbitrary String tag that can be
* used to group together runs during later analysis. One use of this capability is to tag runs as GATK
* performance tests, so that the performance of the GATK over time can be assessed from the logs directly.
*
* Note that the tags do not conform to any ontology, so you are free to use any tags that you might find
* meaningful.
*/
@Argument(fullName = "tag", shortName = "tag", doc="Arbitrary tag string to identify this GATK run as part of a group of runs, for later analysis", required = false)
public String tag = "NA";
// --------------------------------------------------------------------------------------------------------------
//
// XXX
//
// --------------------------------------------------------------------------------------------------------------
@Argument(fullName = "read_filter", shortName = "rf", doc = "Specify filtration criteria to apply to each read individually", required = false)
public List<String> readFilters = new ArrayList<String>();

5
public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
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@ -138,6 +138,9 @@ public class GATKRunReport {
@Element(required = true, name = "iterations")
private long nIterations;
@Element(required = true, name = "tag")
private String tag;
public enum PhoneHomeOption {
/** Disable phone home */
NO_ET,
@ -186,6 +189,8 @@ public class GATKRunReport {
nIterations = engine.getCumulativeMetrics().getNumIterations();
}
tag = engine.getArguments().tag;
// user and hostname -- information about the runner of the GATK
userName = System.getProperty("user.name");
hostName = Utils.resolveHostname();