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Generalized the default platform parameter in BQSRv2 

Parameter wasn't working outside of the BQSR walker. It now takes the information on the recalibration report in other tools (PrintReads for example) and treats all reads as coming from the defined default platform.
This commit is contained in:
Mauricio Carneiro 2012-07-18 14:20:48 -04:00
parent 5dc2143142
commit 921eaad33f
1 changed files with 5 additions and 1 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java
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@ -49,6 +49,7 @@ public class CycleCovariate implements StandardCovariate {
private static final int MAXIMUM_CYCLE_VALUE = 1000;
private static final int CUSHION_FOR_INDELS = 4;
private static String default_platform = null;
private static final EnumSet<NGSPlatform> DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS);
private static final EnumSet<NGSPlatform> FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454, NGSPlatform.ION_TORRENT);
@ -58,13 +59,16 @@ public class CycleCovariate implements StandardCovariate {
public void initialize(final RecalibrationArgumentCollection RAC) {
if (RAC.DEFAULT_PLATFORM != null && !NGSPlatform.isKnown(RAC.DEFAULT_PLATFORM))
throw new UserException.CommandLineException("The requested default platform (" + RAC.DEFAULT_PLATFORM + ") is not a recognized platform.");
if (RAC.DEFAULT_PLATFORM != null)
default_platform = RAC.DEFAULT_PLATFORM;
}
// Used to pick out the covariate's value from attributes of the read
@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
final int readLength = read.getReadLength();
final NGSPlatform ngsPlatform = read.getNGSPlatform();
final NGSPlatform ngsPlatform = default_platform == null ? read.getNGSPlatform() : NGSPlatform.fromReadGroupPL(default_platform);
// Discrete cycle platforms
if (DISCRETE_CYCLE_PLATFORMS.contains(ngsPlatform)) {