zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Support for selecting only variants with specific IDs from a file in SelectVariants 

-- Cleaned up unused variables as well
This commit is contained in:
Mark DePristo 2011-12-16 16:10:18 -05:00
parent d6d2f49c88
commit b6067be952
1 changed files with 47 additions and 40 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

49
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.MendelianViolation;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.variantcontext.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
@ -42,6 +43,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.SampleUtils;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.util.*;
@ -140,7 +142,7 @@ import java.util.*;
* -R ref.fasta \
* -T SelectVariants \
* --variant input.vcf \
* -family NA12891+NA12892=NA12878 \
* -bed family.ped \
* -mvq 50 \
* -o violations.vcf
*
@ -250,16 +252,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
@Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Don't update the AC, AF, or AN values in the INFO field after selecting", required=false)
private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
@Hidden
@Argument(fullName="family_structure_file", shortName="familyFile", doc="use -family unless you know what you're doing", required=false)
private File FAMILY_STRUCTURE_FILE = null;
/**
* String formatted as dad+mom=child where these parameters determine which sample names are examined.
*/
@Argument(fullName="family_structure", shortName="family", doc="string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false)
private String FAMILY_STRUCTURE = "";
/**
* This activates the mendelian violation module that will select all variants that correspond to a mendelian violation following the rules given by the family structure.
*/
@ -293,6 +285,14 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
@Argument(fullName="selectTypeToInclude", shortName="selectType", doc="Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times", required=false)
private List<VariantContext.Type> TYPES_TO_INCLUDE = new ArrayList<VariantContext.Type>();
/**
* If provided, we will only include variants whose ID field is present in this list of ids. The matching
* is exact string matching. The file format is just one ID per line
*
*/
@Argument(fullName="keepIDs", shortName="IDs", doc="Only emit sites whose ID is found in this file (one ID per line)", required=false)
private File rsIDFile = null;
@Hidden
@Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false)
@ -339,17 +339,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
private int positionToAdd = 0;
private RandomVariantStructure [] variantArray;
/* Variables used for random selection with AF boosting */
private ArrayList<Double> afBreakpoints = null;
private ArrayList<Double> afBoosts = null;
double bkDelta = 0.0;
private PrintStream outMVFileStream = null;
//Random number generator for the genotypes to remove
private Random randomGenotypes = new Random();
private Set<String> IDsToKeep = null;
/**
* Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
*/
@ -437,7 +433,18 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
if (SELECT_RANDOM_FRACTION) logger.info("Selecting approximately " + 100.0*fractionRandom + "% of the variants at random from the variant track");
/** load in the IDs file to a hashset for matching */
if ( rsIDFile != null ) {
IDsToKeep = new HashSet<String>();
try {
for ( final String line : new XReadLines(rsIDFile).readLines() ) {
IDsToKeep.add(line.trim());
}
logger.info("Selecting only variants with one of " + IDsToKeep.size() + " IDs from " + rsIDFile);
} catch ( FileNotFoundException e ) {
throw new UserException.CouldNotReadInputFile(rsIDFile, e);
}
}
}
/**
@ -460,6 +467,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
}
for (VariantContext vc : vcs) {
if ( IDsToKeep != null && ! IDsToKeep.contains(vc.getID()) )
continue;
if (MENDELIAN_VIOLATIONS && mv.countViolations(this.getSampleDB().getFamilies(samples),vc) < 1)
break;
@ -513,10 +523,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
vcfWriter.add(sub);
}
}
}
return 1;