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By default, don't quantize quals in BQSRv2

This commit is contained in:
Eric Banks 2012-07-14 23:49:48 -04:00
parent 75543a3f22
commit f29cadd7e2
1 changed files with 3 additions and 3 deletions
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public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -203,11 +203,11 @@ public class GATKArgumentCollection {
* Turns on the base quantization module. It requires a recalibration report (-BQSR). * Turns on the base quantization module. It requires a recalibration report (-BQSR).
* *
* A value of 0 here means "do not quantize". * A value of 0 here means "do not quantize".
* Any value greater than zero will be used to recalculate the quantization using this many levels. * Any value greater than zero will be used to recalculate the quantization using that many levels.
* Negative values do nothing (i.e. quantize using the recalibration report's quantization level -- same as not providing this parameter at all) * Negative values mean that we should quantize using the recalibration report's quantization level.
*/ */
@Argument(fullName="quantize_quals", shortName = "qq", doc = "Quantize quality scores to a given number of levels.", required=false) @Argument(fullName="quantize_quals", shortName = "qq", doc = "Quantize quality scores to a given number of levels.", required=false)
public int quantizationLevels = -1; public int quantizationLevels = 0;
/** /**
* Turns off printing of the base insertion and base deletion tags when using the -BQSR argument. Only the base substitution qualities will be produced. * Turns off printing of the base insertion and base deletion tags when using the -BQSR argument. Only the base substitution qualities will be produced.