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Add option to specify maximum STR length to RepeatCovariates from command line to ease testing

This commit is contained in:
Guillermo del Angel 2013-02-01 11:13:10 -05:00
parent 75ceddf9e5
commit baf2c4c338
3 changed files with 19 additions and 5 deletions
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12
protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
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@ -223,6 +223,18 @@ public class RecalibrationArgumentCollection {
@Output(fullName = "recal_table_update_log", shortName = "recal_table_update_log", required = false, doc = "If provided, log all updates to the recalibration tables to the given file. For debugging/testing purposes only")
public PrintStream RECAL_TABLE_UPDATE_LOG = null;
/**
* The repeat covariate will use a context of this size to calculate it's covariate value for base insertions and deletions
*/
@Hidden
@Argument(fullName = "max_str_unit_length", shortName = "maxstr", doc = "Max size of the k-mer context to be used for repeat covariates", required = false)
public int MAX_STR_UNIT_LENGTH = 8;
@Hidden
@Argument(fullName = "max_repeat_length", shortName = "maxrep", doc = "Max number of repetitions to be used for repeat covariates", required = false)
public int MAX_REPEAT_LENGTH = 20;
public File existingRecalibrationReport = null;
public GATKReportTable generateReportTable(final String covariateNames) {

6
protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java
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@ -61,8 +61,8 @@ import java.util.Map;
import java.util.Set;
public abstract class RepeatCovariate implements ExperimentalCovariate {
public static final int MAX_REPEAT_LENGTH = 20;
public static final int MAX_STR_UNIT_LENGTH = 8;
protected int MAX_REPEAT_LENGTH;
protected int MAX_STR_UNIT_LENGTH;
private final HashMap<String, Integer> repeatLookupTable = new HashMap<String, Integer>();
private final HashMap<Integer, String> repeatReverseLookupTable = new HashMap<Integer, String>();
private int nextId = 0;
@ -70,6 +70,8 @@ public abstract class RepeatCovariate implements ExperimentalCovariate {
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize(final RecalibrationArgumentCollection RAC) {
MAX_STR_UNIT_LENGTH = RAC.MAX_STR_UNIT_LENGTH;
MAX_REPEAT_LENGTH = RAC.MAX_REPEAT_LENGTH;
}
@Override

6
protected/java/test/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java
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@ -139,8 +139,8 @@ public class RepeatCovariatesUnitTest {
@Test(enabled = true)
public void testManyObservations() {
final int NUM_UNITS = 10;
final int MAX_REPEAT_UNIT_LENGTH = RepeatCovariate.MAX_STR_UNIT_LENGTH;
final int MAX_NUM_REPETITIONS = RepeatCovariate.MAX_REPEAT_LENGTH;
final int MAX_REPEAT_UNIT_LENGTH = RAC.MAX_STR_UNIT_LENGTH;
final int MAX_NUM_REPETITIONS = RAC.MAX_REPEAT_LENGTH;
final int NUM_TEST_CASES = 100;
Random random = new Random();
@ -207,7 +207,7 @@ public class RepeatCovariatesUnitTest {
int fw = GATKVariantContextUtils.findNumberofRepetitions(ruValM.getBytes(), readBases.substring(offset+1,readLength).getBytes(),true);
int bw = GATKVariantContextUtils.findNumberofRepetitions(ruValM.getBytes(), readBases.substring(0,offset+1).getBytes(),false);
Assert.assertEquals(Math.min(fw+bw,RepeatCovariate.MAX_REPEAT_LENGTH),(int)Integer.valueOf(rlValM));
Assert.assertEquals(Math.min(fw+bw,RAC.MAX_REPEAT_LENGTH),(int)Integer.valueOf(rlValM));
}
}