zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Allow debugging to be set from the command line

This commit is contained in:
Menachem Fromer 2012-11-27 22:37:41 -05:00
parent 31069ffced
commit 79bc878e6a
1 changed files with 5 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
View File

@ -95,7 +95,8 @@ import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFr
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingStats> {
private static final boolean DEBUG = false;
@Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information (if -l DEBUG is also specified)", required = false)
protected boolean DEBUG = false;
/**
* The VCF file we are phasing variants from.
*
@ -949,7 +950,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
}
if (DEBUG) logger.debug("\nPhasing table [AFTER CALCULATION]:\n" + sampleHaps + "\n");
MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, true);
MaxHaplotypeAndQuality maxHapQual = new MaxHaplotypeAndQuality(sampleHaps, DEBUG);
double posteriorProb = maxHapQual.maxEntry.getScore().getValue();
if (DEBUG)
@ -971,7 +972,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
public MaxHaplotypeAndQuality(PhasingTable hapTable, boolean printDebug) {
// Marginalize each haplotype to its first 2 positions:
hapTable = HaplotypeTableCreator.marginalizeAsNewTable(hapTable);
if (DEBUG && printDebug)
if (printDebug)
logger.debug("\nPhasing table [AFTER MAPPING]:\n" + hapTable + "\n");
calculateMaxHapAndPhasingQuality(hapTable, printDebug);
@ -981,7 +982,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
private void calculateMaxHapAndPhasingQuality(PhasingTable hapTable, boolean printDebug) {
hapTable.normalizeScores();
if (DEBUG && printDebug)
if (printDebug)
logger.debug("\nPhasing table [AFTER NORMALIZATION]:\n" + hapTable + "\n");
// Determine the phase at this position: