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

Added keepOriginalDP argument to SelectVariants 

Fixes #830
This commit is contained in:
Phillip Dexheimer 2015-03-25 22:45:31 -04:00
parent a77c8dd421
commit c97c253ec8
4 changed files with 34 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -290,6 +290,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testKeepOriginalACAndENV--" + testFile, spec);
}
@Test
public void testKeepOriginalDP() {
String testFile = privateTestDir + "CEUtrioTest.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants --keepOriginalDP -R " + b37KGReference + " -sn NA12892 --variant " + testFile + " -o %s --no_cmdline_in_header",
1,
Arrays.asList("e897097a47aee5516dc4f1c0b9d69037")
);
executeTest("testKeepOriginalDP--" + testFile, spec);
}
@Test
public void testMultipleRecordsAtOnePosition() {
String testFile = privateTestDir + "selectVariants.onePosition.vcf";

30
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
View File

@ -214,7 +214,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
protected VariantContextWriter vcfWriter = null;
@Argument(fullName="sample_name", shortName="sn", doc="Include genotypes from this sample. Can be specified multiple times", required=false)
public Set<String> sampleNames = new HashSet<String>(0);
public Set<String> sampleNames = new HashSet<>(0);
@Argument(fullName="sample_expressions", shortName="se", doc="Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times", required=false)
public Set<String> sampleExpressions ;
@ -226,19 +226,19 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
* Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.
*/
@Argument(fullName="exclude_sample_name", shortName="xl_sn", doc="Exclude genotypes from this sample. Can be specified multiple times", required=false)
public Set<String> XLsampleNames = new HashSet<String>(0);
public Set<String> XLsampleNames = new HashSet<>(0);
/**
* Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.
*/
@Input(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false)
public Set<File> XLsampleFiles = new HashSet<File>(0);
public Set<File> XLsampleFiles = new HashSet<>(0);
/**
* Note that these expressions are evaluated *after* the specified samples are extracted and the INFO field annotations are updated.
*/
@Argument(shortName="select", doc="One or more criteria to use when selecting the data", required=false)
public ArrayList<String> SELECT_EXPRESSIONS = new ArrayList<String>();
public ArrayList<String> SELECT_EXPRESSIONS = new ArrayList<>();
@Argument(fullName="excludeNonVariants", shortName="env", doc="Don't include loci found to be non-variant after the subsetting procedure", required=false)
protected boolean EXCLUDE_NON_VARIANTS = false;
@ -276,6 +276,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
@Argument(fullName="keepOriginalAC", shortName="keepOriginalAC", doc="Store the original AC, AF, and AN values in the INFO field after selecting (using keys AC_Orig, AF_Orig, and AN_Orig)", required=false)
private boolean KEEP_ORIGINAL_CHR_COUNTS = false;
@Argument(fullName="keepOriginalDP", shortName="keepOriginalDP", doc="Store the original DP value in the INFO field (using the DP_Orig key) after selecting", required=false)
private boolean KEEP_ORIGINAL_DEPTH = false;
/**
* 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.
*/
@ -300,7 +303,7 @@ 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>();
private List<VariantContext.Type> TYPES_TO_INCLUDE = new ArrayList<>();
/**
* If provided, we will only include variants whose ID field is present in this list of ids. The matching
@ -336,11 +339,11 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
MULTIALLELIC
}
private ArrayList<VariantContext.Type> selectedTypes = new ArrayList<VariantContext.Type>();
private ArrayList<String> selectNames = new ArrayList<String>();
private ArrayList<VariantContext.Type> selectedTypes = new ArrayList<>();
private ArrayList<String> selectNames = new ArrayList<>();
private List<VariantContextUtils.JexlVCMatchExp> jexls = null;
private TreeSet<String> samples = new TreeSet<String>();
private TreeSet<String> samples = new TreeSet<>();
private boolean NO_SAMPLES_SPECIFIED = false;
private boolean DISCORDANCE_ONLY = false;
@ -366,13 +369,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
List<String> rodNames = Arrays.asList(variantCollection.variants.getName());
vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
TreeSet<String> vcfSamples = new TreeSet<>(SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
Collection<String> samplesFromExpressions = SampleUtils.matchSamplesExpressions(vcfSamples, sampleExpressions);
// first, check overlap between requested and present samples
Set<String> commandLineUniqueSamples = new HashSet<String>(samplesFromFile.size()+samplesFromExpressions.size()+sampleNames.size());
Set<String> commandLineUniqueSamples = new HashSet<>(samplesFromFile.size()+samplesFromExpressions.size()+sampleNames.size());
commandLineUniqueSamples.addAll(samplesFromFile);
commandLineUniqueSamples.addAll(samplesFromExpressions);
commandLineUniqueSamples.addAll(sampleNames);
@ -437,6 +440,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AF_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_AN_KEY));
}
if (KEEP_ORIGINAL_DEPTH)
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.ORIGINAL_DP_KEY));
headerLines.addAll(Arrays.asList(ChromosomeCountConstants.descriptions));
headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY));
@ -464,7 +469,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
/** load in the IDs file to a hashset for matching */
if ( rsIDFile != null ) {
IDsToKeep = new HashSet<String>();
IDsToKeep = new HashSet<>();
try {
for ( final String line : new XReadLines(rsIDFile).readLines() ) {
IDsToKeep.add(line.trim());
@ -788,6 +793,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
VariantContextUtils.calculateChromosomeCounts(builder, false);
if (KEEP_ORIGINAL_DEPTH && originalVC.hasAttribute(VCFConstants.DEPTH_KEY))
builder.attribute(GATKVCFConstants.ORIGINAL_DP_KEY, originalVC.getAttribute(VCFConstants.DEPTH_KEY));
boolean sawDP = false;
int depth = 0;
for ( final String sample : selectedSampleNames ) {

1
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
View File

@ -49,6 +49,7 @@ public final class GATKVCFConstants {
public static final String CLIPPING_RANK_SUM_KEY = "ClippingRankSum";
public static final String CULPRIT_KEY = "culprit";
public static final String SPANNING_DELETIONS_KEY = "Dels";
public static final String ORIGINAL_DP_KEY = "DP_Orig"; //SelectVariants
public static final String DOWNSAMPLED_KEY = "DS";
public static final String FISHER_STRAND_KEY = "FS";
public static final String GC_CONTENT_KEY = "GC";

1
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
View File

@ -129,6 +129,7 @@ public class GATKVCFHeaderLines {
addInfoLine(new VCFInfoHeaderLine(ORIGINAL_AC_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Original AC"));
addInfoLine(new VCFInfoHeaderLine(ORIGINAL_AF_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Original AF"));
addInfoLine(new VCFInfoHeaderLine(ORIGINAL_AN_KEY, 1, VCFHeaderLineType.Integer, "Original AN"));
addInfoLine(new VCFInfoHeaderLine(ORIGINAL_DP_KEY, 1, VCFHeaderLineType.Integer, "Original DP"));
addInfoLine(new VCFInfoHeaderLine(ORIGINAL_CONTIG_KEY, 1, VCFHeaderLineType.String, "Original contig name for the record"));
addInfoLine(new VCFInfoHeaderLine(ORIGINAL_START_KEY, 1, VCFHeaderLineType.Integer, "Original start position for the record"));
addInfoLine(new VCFInfoHeaderLine(VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "Log odds ratio of being a true variant versus being false under the trained gaussian mixture model"));