Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Ryan Poplin
commit
4b18786b5d
29
build.xml
29
build.xml
|
|
@ -281,6 +281,10 @@
|
|||
<equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
|
||||
</condition>
|
||||
|
||||
<condition property="include.external">
|
||||
<available file="${external.dir}"/>
|
||||
</condition>
|
||||
|
||||
<condition property="include.contracts">
|
||||
<equals arg1="${use.contracts}" arg2="true" />
|
||||
</condition>
|
||||
|
|
@ -331,7 +335,7 @@
|
|||
</javac>
|
||||
</target>
|
||||
|
||||
<target name="gatk.compile.external.source" depends="gatk.compile.public.source,gatk.compile.private.source">
|
||||
<target name="gatk.compile.external.source" depends="gatk.compile.public.source,gatk.compile.private.source" if="include.external">
|
||||
<subant target="compile" genericantfile="build.xml">
|
||||
<property name="build.dir" value="${external.build.dir}" />
|
||||
<property name="dist.dir" value="${external.dist.dir}" />
|
||||
|
|
@ -761,6 +765,7 @@
|
|||
<property name="java.test.classes" value="${build.dir}/java/testclasses"/>
|
||||
<property name="java.public.test.classes" value="${java.test.classes}/public"/>
|
||||
<property name="java.private.test.classes" value="${java.test.classes}/private"/>
|
||||
<property name="java.external.test.classes" value="${java.test.classes}/external"/>
|
||||
<property name="java.public.test.sources" value="${public.dir}/java/test"/>
|
||||
<property name="java.private.test.sources" value="${private.dir}/java/test"/>
|
||||
<property name="scala.test.classes" value="${build.dir}/scala/testclasses"/>
|
||||
|
|
@ -811,7 +816,23 @@
|
|||
</javac>
|
||||
</target>
|
||||
|
||||
<target name="test.java.compile" depends="test.java.public.compile, test.java.private.compile"/>
|
||||
<target name="test.java.external.compile" depends="dist,test.init.compile,test.java.public.compile" if="include.external">
|
||||
<mkdir dir="${java.external.test.classes}"/>
|
||||
<echo message="Sting: Compiling external test cases!"/>
|
||||
<javac fork="true" memoryMaximumSize="512m" destdir="${java.external.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}" srcdir="${external.dir}">
|
||||
<include name="*/test/**/*.java"/>
|
||||
<classpath>
|
||||
<path refid="external.dependencies" />
|
||||
<pathelement location="${java.public.test.classes}"/>
|
||||
<pathelement location="${java.classes}"/>
|
||||
<pathelement location="${java.contracts}"/>
|
||||
<pathelement location="${testng.jar}"/>
|
||||
</classpath>
|
||||
<compilerarg value="-proc:none"/>
|
||||
</javac>
|
||||
</target>
|
||||
|
||||
<target name="test.java.compile" depends="test.java.public.compile, test.java.private.compile, test.java.external.compile"/>
|
||||
|
||||
<target name="test.scala.public.compile" depends="test.java.compile,scala.compile" if="scala.include">
|
||||
<mkdir dir="${scala.public.test.classes}"/>
|
||||
|
|
@ -852,6 +873,7 @@
|
|||
<pathelement location="${java.contracts}" />
|
||||
<pathelement location="${java.public.test.classes}" />
|
||||
<pathelement location="${java.private.test.classes}" />
|
||||
<pathelement location="${java.external.test.classes}" />
|
||||
<pathelement location="${scala.public.test.classes}" />
|
||||
<pathelement location="${scala.private.test.classes}" />
|
||||
<pathelement location="${R.tar.dir}" />
|
||||
|
|
@ -934,6 +956,9 @@
|
|||
<classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
|
||||
<include name="**/@{testtype}.class" if="include.private"/>
|
||||
</classfileset>
|
||||
<classfileset dir="${java.external.test.classes}" erroronmissingdir="false">
|
||||
<include name="**/@{testtype}.class" if="include.external"/>
|
||||
</classfileset>
|
||||
<classfileset dir="${scala.public.test.classes}" erroronmissingdir="false">
|
||||
<include name="**/@{testtype}*.class" if="scala.include"/>
|
||||
</classfileset>
|
||||
|
|
|
|||
|
|
@ -54,7 +54,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
|
|||
private static final double MIN_PVALUE = 1E-320;
|
||||
|
||||
public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
|
||||
if ( ! vc.isVariant() || vc.isFiltered() )
|
||||
if ( !vc.isVariant() )
|
||||
return null;
|
||||
|
||||
int[][] table;
|
||||
|
|
|
|||
|
|
@ -139,6 +139,12 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
|
|||
@Argument(fullName="missingValuesInExpressionsShouldEvaluateAsFailing", doc="When evaluating the JEXL expressions, missing values should be considered failing the expression", required=false)
|
||||
protected Boolean FAIL_MISSING_VALUES = false;
|
||||
|
||||
/**
|
||||
* Invalidate previous filters applied to the VariantContext, applying only the filters here
|
||||
*/
|
||||
@Argument(fullName="invalidatePreviousFilters",doc="Remove previous filters applied to the VCF",required=false)
|
||||
boolean invalidatePrevious = false;
|
||||
|
||||
// JEXL expressions for the filters
|
||||
List<VariantContextUtils.JexlVCMatchExp> filterExps;
|
||||
List<VariantContextUtils.JexlVCMatchExp> genotypeFilterExps;
|
||||
|
|
@ -215,6 +221,9 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
|
|||
|
||||
for ( VariantContext vc : VCs ) {
|
||||
|
||||
if ( invalidatePrevious ) {
|
||||
vc = (new VariantContextBuilder(vc)).filters(new HashSet<String>()).make();
|
||||
}
|
||||
// filter based on previous mask position
|
||||
if ( previousMaskPosition != null && // we saw a previous mask site
|
||||
previousMaskPosition.getContig().equals(vc.getChr()) && // it's on the same contig
|
||||
|
|
|
|||
|
|
@ -155,7 +155,9 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
|
|||
/////////////////////////////
|
||||
/**
|
||||
* This algorithm treats every reference mismatch as an indication of error. However, real genetic variation is expected to mismatch the reference,
|
||||
* so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites.
|
||||
* so it is critical that a database of known polymorphic sites is given to the tool in order to skip over those sites. This tool accepts any number of RodBindings (VCF, Bed, etc.)
|
||||
* for use as this database. For users wishing to exclude an interval list of known variation simply use -XL my.interval.list to skip over processing those sites.
|
||||
* Please note however that the statistics reported by the tool will not accurately reflected those sites skipped by the -XL argument.
|
||||
*/
|
||||
@Input(fullName="knownSites", shortName = "knownSites", doc="A database of known polymorphic sites to skip over in the recalibration algorithm", required=false)
|
||||
public List<RodBinding<Feature>> knownSites = Collections.emptyList();
|
||||
|
|
|
|||
|
|
@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
|
|||
|
||||
import org.apache.log4j.Logger;
|
||||
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
|
|
@ -126,7 +125,7 @@ public class VariantRecalibratorEngine {
|
|||
iteration++;
|
||||
model.maximizationStep( data );
|
||||
currentChangeInMixtureCoefficients = model.normalizePMixtureLog10();
|
||||
model.expectationStep(data);
|
||||
model.expectationStep( data );
|
||||
if( iteration % 5 == 0 ) { // cut down on the number of output lines so that users can read the warning messages
|
||||
logger.info("Finished iteration " + iteration + ". \tCurrent change in mixture coefficients = " + String.format("%.5f", currentChangeInMixtureCoefficients));
|
||||
}
|
||||
|
|
|
|||
|
|
@ -105,7 +105,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
|
|||
* and each named argument will be labeled as such in the output (i.e., set=name rather than
|
||||
* set=variants2). The order of arguments does not matter unless except for the naming, so
|
||||
* if you provide an rod priority list and no explicit names than variants, variants2, etc
|
||||
* are techincally order dependent. It is strongly recommended to provide explicit names when
|
||||
* are technically order dependent. It is strongly recommended to provide explicit names when
|
||||
* a rod priority list is provided.
|
||||
*/
|
||||
@Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
|
||||
|
|
|
|||
|
|
@ -1569,4 +1569,48 @@ public class MathUtils {
|
|||
}
|
||||
return shuffled;
|
||||
}
|
||||
|
||||
/**
|
||||
* Vector operations
|
||||
*/
|
||||
public static double[] vectorSum(double v1[], double v2[]) {
|
||||
if (v1.length != v2.length)
|
||||
throw new UserException("BUG: vectors v1, v2 of different size in vectorSum()");
|
||||
|
||||
double result[] = new double[v1.length];
|
||||
for (int k=0; k < v1.length; k++)
|
||||
result[k] = v1[k]+v2[k];
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
public static double[] scalarTimesIntVector(double a, int[] v1) {
|
||||
|
||||
double result[] = new double[v1.length];
|
||||
for (int k=0; k < v1.length; k++)
|
||||
result[k] = a*v1[k];
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
public static double dotProduct(double v1[], double v2[]) {
|
||||
if (v1.length != v2.length)
|
||||
throw new UserException("BUG: vectors v1, v2 of different size in vectorSum()");
|
||||
|
||||
double result = 0.0;
|
||||
for (int k=0; k < v1.length; k++)
|
||||
result += v1[k]*v2[k];
|
||||
|
||||
return result;
|
||||
|
||||
}
|
||||
|
||||
public static double[] vectorLog10(double v1[]) {
|
||||
double result[] = new double[v1.length];
|
||||
for (int k=0; k < v1.length; k++)
|
||||
result[k] = Math.log10(v1[k]);
|
||||
|
||||
return result;
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -608,7 +608,7 @@ public class ReadUtils {
|
|||
* Example: Locus => {read1, read2, ..., readN}
|
||||
*
|
||||
* - Second: readToLocusMap -- a HashMap that describes for each read what loci it contributes to the coverage.
|
||||
* Note: Locus is a boolean array, indexed from 0 (= startLocation) to N (= stopLocation), with true meaning it contributes to the coverage.
|
||||
* Note: Locus is a boolean array, indexed from 0 (= startLocation) to N (= stopLocation), with value==true meaning it contributes to the coverage.
|
||||
* Example: Read => {true, true, false, ... false}
|
||||
*
|
||||
* @param readList the list of reads to generate the association mappings
|
||||
|
|
|
|||
|
|
@ -464,7 +464,11 @@ public class VariantContextUtils {
|
|||
/**
|
||||
* Requires all records present at site to be unfiltered. VCF files that don't contain the record don't influence this.
|
||||
*/
|
||||
KEEP_IF_ALL_UNFILTERED
|
||||
KEEP_IF_ALL_UNFILTERED,
|
||||
/**
|
||||
* If any record is present at this site (regardless of possibly being filtered), then all such records are kept and the filters are reset.
|
||||
*/
|
||||
KEEP_UNCONDITIONAL
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -635,7 +639,7 @@ public class VariantContextUtils {
|
|||
}
|
||||
|
||||
// if at least one record was unfiltered and we want a union, clear all of the filters
|
||||
if ( filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size() )
|
||||
if ( (filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size()) || filteredRecordMergeType == FilteredRecordMergeType.KEEP_UNCONDITIONAL )
|
||||
filters.clear();
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testWithAllelesPassedIn2() {
|
||||
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
|
||||
Arrays.asList("43e7a17d95b1a0cf72e669657794d802"));
|
||||
Arrays.asList("1899bdb956c62bbcbf160b18cd3aea60"));
|
||||
executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
|
||||
}
|
||||
|
||||
|
|
@ -275,7 +275,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
|
||||
+ validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation +
|
||||
"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
|
||||
Arrays.asList("36ce53ae4319718ad9c8ae391deebc8c"));
|
||||
Arrays.asList("320f61c87253aba77d6dc782242cba8b"));
|
||||
executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec2);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -26,23 +26,23 @@ class VCFExtractIntervals(inVCF: File, outList: File, useFilterSites: Boolean) e
|
|||
var cur : String = null
|
||||
if ( elems.hasNext ) {
|
||||
cur = elems.next
|
||||
} else {
|
||||
out.printf("%s%n",prev)
|
||||
}
|
||||
while ( elems.hasNext ) {
|
||||
out.printf("%s%n",prev)
|
||||
while ( cur.equals(prev) && elems.hasNext && !cur.equals("") ) {
|
||||
cur = elems.next
|
||||
}
|
||||
|
||||
if ( ! cur.equals(prev) ) {
|
||||
if ( elems.hasNext ) {
|
||||
prev = cur
|
||||
while ( elems.hasNext ) {
|
||||
out.printf("%s%n",prev)
|
||||
while ( cur.equals(prev) && elems.hasNext && !cur.equals("") ) {
|
||||
cur = elems.next
|
||||
} else {
|
||||
out.printf("%s%n",cur)
|
||||
}
|
||||
|
||||
if ( ! cur.equals(prev) ) {
|
||||
if ( elems.hasNext ) {
|
||||
prev = cur
|
||||
cur = elems.next
|
||||
}
|
||||
}
|
||||
}
|
||||
out.printf("%s%n",prev)
|
||||
out.printf("%s%n",cur)
|
||||
} else {
|
||||
out.printf("%s%n",prev)
|
||||
}
|
||||
|
||||
out.close
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ import collection.JavaConversions._
|
|||
import org.broadinstitute.sting.commandline._
|
||||
import java.io.{PrintWriter, PrintStream, File}
|
||||
|
||||
class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extends InProcessFunction {
|
||||
class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extends InProcessFunction {
|
||||
def this(in: File, out: File, samples: File) = this(in,out, (new XReadLines(samples)).readLines.toList)
|
||||
|
||||
@Input(doc="VCF from which to extract samples") var inputVCF : File = inVCF
|
||||
|
|
|
|||
Loading…
Reference in New Issue