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Misc cleanup of UG args 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2620 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-01-17 04:38:52 +00:00
parent a57886ab81
commit 12453fa163
5 changed files with 16 additions and 61 deletions
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1
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
View File

@ -70,7 +70,6 @@ public abstract class GenotypeCalculationModel implements Cloneable {
GENOTYPE_MODE = UAC.GENOTYPE;
POOL_SIZE = UAC.POOLSIZE;
CONFIDENCE_THRESHOLD = UAC.CONFIDENCE_THRESHOLD;
MINIMUM_ALLELE_FREQUENCY = UAC.MINIMUM_ALLELE_FREQUENCY;
REPORT_SLOD = ! UAC.NO_SLOD;
this.verboseWriter = verboseWriter;
this.beagleWriter = beagleWriter;

28
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
View File

@ -228,34 +228,6 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
PofFs[baseIndex] = Math.min(sum, 1.0); // deal with precision errors
}
/***
protected double[] getHardyWeinbergValues(double f) {
double[] HWvalues = hardyWeinbergValueCache.get(f);
// if it hasn't been calculated yet, do so now
if ( HWvalues == null ) {
// create Hardy-Weinberg based allele frequencies (p^2, 2pq, q^2) converted to log-space
double p = 1.0 - f;
double q = f;
// allele frequencies don't actually equal 0...
if ( MathUtils.compareDoubles(q, 0.0) == 0 ) {
q = MINIMUM_ALLELE_FREQUENCY;
p -= MINIMUM_ALLELE_FREQUENCY;
} else if ( MathUtils.compareDoubles(p, 0.0) == 0 ) {
p = MINIMUM_ALLELE_FREQUENCY;
q -= MINIMUM_ALLELE_FREQUENCY;
}
HWvalues = new double[] { Math.pow(p, 2), 2.0 * p * q, Math.pow(q, 2) };
hardyWeinbergValueCache.put(f, HWvalues);
}
return HWvalues;
}
***/
/**
* @param ref the ref base
* @param loc the GenomeLoc

6
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -66,9 +66,6 @@ public class UnifiedArgumentCollection {
// control the various parameters to be used
@Argument(fullName = "lod_threshold", shortName = "lod", doc = "[DEPRECATED] The lod threshold by which variants should be filtered", required = false)
public double LOD_THRESHOLD = Double.MIN_VALUE;
@Argument(fullName = "min_confidence_threshold", shortName = "confidence", doc = "The phred-scaled confidence threshold by which variants should be filtered", required = false)
public double CONFIDENCE_THRESHOLD = 0.0;
@ -89,7 +86,4 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "max_coverage", shortName = "mc", doc = "Maximum reads at this locus for it to be callable; to disable, provide value < 1 [default:10,000]", required = false)
public Integer MAX_READS_IN_PILEUP = 10000;
@Argument(fullName = "min_allele_frequency", shortName = "min_freq", doc = "The minimum possible allele frequency in a population (advanced)", required = false)
public double MINIMUM_ALLELE_FREQUENCY = 1e-8;
}

16
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -96,22 +96,12 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
if ( UAC.POOLSIZE < 1 && UAC.genotypeModel == GenotypeCalculationModel.Model.POOLED ) {
throw new IllegalArgumentException("Attempting to use the POOLED model with a pool size less than 1. Please set the pool size to an appropriate value.");
}
if ( UAC.LOD_THRESHOLD != Double.MIN_VALUE ) {
StringBuilder sb = new StringBuilder();
sb.append("\n***\tThe --lod_threshold argument is no longer supported; instead, please use --min_confidence_threshold.");
sb.append("\n***\tThere is approximately a 10-to-1 mapping from confidence to LOD.");
sb.append("\n***\tUse Q" + (10.0 * UAC.LOD_THRESHOLD) + " as an approximate equivalent to your LOD " + UAC.LOD_THRESHOLD + " cutoff");
throw new IllegalArgumentException(sb.toString());
}
if ( beagleWriter != null && UAC.genotypeModel == GenotypeCalculationModel.Model.EM_POINT_ESTIMATE ) {
throw new IllegalArgumentException("BEAGLE output is not currently supported in the EM_POINT_ESTIMATE calculation model.");
}
// some arguments can't be handled (at least for now) while we are multi-threaded
if ( getToolkit().getArguments().numberOfThreads > 1 ) {
// no ASSUME_SINGLE_SAMPLE because the IO system doesn't know how to get the sample name
if ( UAC.ASSUME_SINGLE_SAMPLE != null )
throw new IllegalArgumentException("For technical reasons, the ASSUME_SINGLE_SAMPLE argument cannot be used with multiple threads");
if ( getToolkit().getArguments().numberOfThreads > 1 && UAC.ASSUME_SINGLE_SAMPLE != null ) {
// the ASSUME_SINGLE_SAMPLE argument can't be handled (at least for now) while we are multi-threaded because the IO system doesn't know how to get the sample name
throw new IllegalArgumentException("For technical reasons, the ASSUME_SINGLE_SAMPLE argument cannot be used with multiple threads");
}
// get all of the unique sample names - unless we're in POOLED mode, in which case we ignore the sample names

26
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -22,7 +22,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1PointEM() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
Arrays.asList("f033627f849ca8148fe4168c8172eb32"));
Arrays.asList("6a36a1237b1f2b704c682ac947aeb692"));
executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
}
@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2PointEM() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
Arrays.asList("2d181aa420f200fb19a0b5f40855dfd7"));
Arrays.asList("4f221d23a8c218ea592fb7158736a407"));
executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
}
@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testPooled1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
Arrays.asList("1fc421c8e5ccba7ba2f803fc17c27565"));
Arrays.asList("e344fa16b155be00bc4d9b8cc3221187"));
executeTest("testPooled1", spec);
}
@ -56,7 +56,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
Arrays.asList("b8b937e5d44114c265cfa86dbb5e45c8"));
Arrays.asList("6f85a0d0134675be6fe8d3af9e9f7467"));
executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
}
@ -64,7 +64,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
Arrays.asList("499a589c9da3a6adcccc4561b84dfde1"));
Arrays.asList("4a7e44e834d100b143e52beffdd79d1f"));
executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
}
@ -72,7 +72,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
Arrays.asList("1dc507fbe54e289f18d9738398426050"));
Arrays.asList("d3adfbae8c9d18851cab13659239bc03"));
executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
}
@ -85,7 +85,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testParallelization() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,400,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -nt 4", 1,
Arrays.asList("6ae7741b72024781aa2969c785ede392"));
Arrays.asList("a57dabbe7dd12015759de72fef8bc879"));
executeTest("test parallelization", spec);
}
@ -98,11 +98,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testParameter() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-genotype", "094c15be4f9b7c348a12f4bc27efb6e3" );
e.put( "-all_bases", "0097049976ba72dc70476670f1ab2ec6" );
e.put( "--min_base_quality_score 26", "fa88be0dc1f6807829f15df82d3cf393" );
e.put( "--min_mapping_quality_score 26", "225f47a2f73cd4ca16606e0fcc09ba51" );
e.put( "--max_mismatches_in_40bp_window 5", "d8192dc36ebc205aaaaae7734a6144b5" );
e.put( "-genotype", "65abc7cbf940f89037ec61b764054060" );
e.put( "-all_bases", "ff63408d7b5aeb90bc85e471d9de1390" );
e.put( "--min_base_quality_score 26", "287858958aa8cf3be8b43c12cb317ebc" );
e.put( "--min_mapping_quality_score 26", "4e70544703309610e70164db100c66b7" );
e.put( "--max_mismatches_in_40bp_window 5", "14e17c27b6559f9b98d91842c271db3f" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -116,7 +116,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1,
Arrays.asList("63b37207255069ca47a6ffd77bf562f0"));
Arrays.asList("ae98a5e96af774514eac5dea31078e0c"));
executeTest("testConfidence", spec);
}