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gatk-3.8/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java

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First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
/*
Updated all JAVA file licenses accordingly GSATDG-5
2013-01-11 06:04:08 +08:00
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
package org.broadinstitute.variant.variantcontext;
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
import com.google.caliper.Param;
import com.google.caliper.SimpleBenchmark;
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broadinstitute.sting.utils.GenomeLocParser;
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
import org.broadinstitute.variant.vcf.VCFCodec;
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
Updating to latest google caliper code
2013-01-08 10:25:44 +08:00
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
/**
* Caliper microbenchmark of parsing a VCF file
*/
public class VariantContextBenchmark extends SimpleBenchmark {
@Param({"/Users/depristo/Desktop/broadLocal/localData/ALL.chr20.merged_beagle_mach.20101123.snps_indels_svs.genotypes.vcf"})
String vcfFile;
@Param({"1000"})
int linesToRead; // set automatically by framework
@Param({"100"})
int nSamplesToTake; // set automatically by framework
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
@Param({"10"})
int dupsToMerge; // set automatically by framework
More general handling of parameters for VariantContextBenchmark
2011-11-11 23:22:19 +08:00
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
@Param
Operation operation; // set automatically by framework
More general handling of parameters for VariantContextBenchmark
2011-11-11 23:22:19 +08:00
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
private String INPUT_STRING;
More general handling of parameters for VariantContextBenchmark
2011-11-11 23:22:19 +08:00
public enum Operation {
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
READ,
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
SUBSET_TO_SAMPLES,
GET_TYPE,
GET_ID,
GET_GENOTYPES,
GET_ATTRIBUTE_STRING,
GET_ATTRIBUTE_INT,
GET_N_SAMPLES,
GET_GENOTYPES_FOR_SAMPLES,
GET_GENOTYPES_IN_ORDER_OF_NAME,
CALC_GENOTYPE_COUNTS,
MERGE
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
}
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
private GenomeLocParser b37GenomeLocParser;
More general handling of parameters for VariantContextBenchmark
2011-11-11 23:22:19 +08:00
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
@Override protected void setUp() {
Rev Tribble to r97, adding binary feature support From tribble logs: Binary feature support in tribble -- Massive refactoring and cleanup -- Many bug fixes throughout -- FeatureCodec is now general, with decode etc. taking a PositionBufferedStream as an argument not a String -- See ExampleBinaryCodec for an example binary codec -- AbstractAsciiFeatureCodec provides to its subclass the same String decode, readHeader functionality before. Old ASCII codecs should inherit from this base class, and will work without additional modifications -- Split AsciiLineReader into a position tracking stream (PositionalBufferedStream). The new AsciiLineReader takes as an argument a PositionalBufferedStream and provides the readLine() functionality of before. Could potentially use optimizations (its a TODO in the code) -- The Positional interface includes some more functionality that's now necessary to support the more general decoding of binary features -- FeatureReaders now work using the general FeatureCodec interface, so they can index binary features -- Bugfixes to LinearIndexCreator off by 1 error in setting the end block position -- Deleted VariantType, since this wasn't used anywhere and it's a particularly clean why of thinking about the problem -- Moved DiploidGenotype, which is specific to Gelitext, to the gelitext package -- TabixReader requires an AsciiFeatureCodec as it's currently only implemented to handle line oriented records -- Renamed AsciiFeatureReader to TribbleIndexedFeatureReader now that it handles Ascii and binary features -- Removed unused functions here and there as encountered -- Fixed build.xml to be truly headless -- FeatureCodec readHeader returns a FeatureCodecHeader obtain that contains a value and the position in the file where the header ends (not inclusive). TribbleReaders now skip the header if the position is set, so its no longer necessary, if one implements the general readHeader(PositionalBufferedStream) version to see header lines in the decode functions. Necessary for binary codecs but a nice side benefit for ascii codecs as well -- Cleaned up the IndexFactory interface so there's a truly general createIndex function that takes the enumerated index type. Added a writeIndex() function that writes an index to disk. -- Vastly expanded the index unit tests and reader tests to really test linear, interval, and tabix indexed files. Updated test.bed, and created a tabix version of it as well. -- Significant BinaryFeaturesTest suite. -- Some test files have indent changes
2012-05-03 19:02:28 +08:00
// TODO -- update for new tribble interface
// try {
// ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.b37KGReference));
// b37GenomeLocParser = new GenomeLocParser(seq);
// } catch ( FileNotFoundException e) {
// throw new RuntimeException(e);
// }
//
// // read it into a String so that we don't try to benchmark IO issues
// try {
// FileInputStream s = new FileInputStream(new File(vcfFile));
// AsciiLineReader lineReader = new AsciiLineReader(s);
// int counter = 0;
// StringBuffer sb = new StringBuffer();
// while (counter++ < linesToRead ) {
// String line = lineReader.readLine();
// if ( line == null )
// break;
// sb.append(line + "\n");
// }
// s.close();
// INPUT_STRING = sb.toString();
// } catch (IOException e) {
// throw new RuntimeException(e);
// }
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
}
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
private interface FunctionToBenchmark<T extends Feature> {
public void run(T vc);
}
private <T extends Feature> void runBenchmark(FeatureCodec<T> codec, FunctionToBenchmark<T> func) {
Rev Tribble to r97, adding binary feature support From tribble logs: Binary feature support in tribble -- Massive refactoring and cleanup -- Many bug fixes throughout -- FeatureCodec is now general, with decode etc. taking a PositionBufferedStream as an argument not a String -- See ExampleBinaryCodec for an example binary codec -- AbstractAsciiFeatureCodec provides to its subclass the same String decode, readHeader functionality before. Old ASCII codecs should inherit from this base class, and will work without additional modifications -- Split AsciiLineReader into a position tracking stream (PositionalBufferedStream). The new AsciiLineReader takes as an argument a PositionalBufferedStream and provides the readLine() functionality of before. Could potentially use optimizations (its a TODO in the code) -- The Positional interface includes some more functionality that's now necessary to support the more general decoding of binary features -- FeatureReaders now work using the general FeatureCodec interface, so they can index binary features -- Bugfixes to LinearIndexCreator off by 1 error in setting the end block position -- Deleted VariantType, since this wasn't used anywhere and it's a particularly clean why of thinking about the problem -- Moved DiploidGenotype, which is specific to Gelitext, to the gelitext package -- TabixReader requires an AsciiFeatureCodec as it's currently only implemented to handle line oriented records -- Renamed AsciiFeatureReader to TribbleIndexedFeatureReader now that it handles Ascii and binary features -- Removed unused functions here and there as encountered -- Fixed build.xml to be truly headless -- FeatureCodec readHeader returns a FeatureCodecHeader obtain that contains a value and the position in the file where the header ends (not inclusive). TribbleReaders now skip the header if the position is set, so its no longer necessary, if one implements the general readHeader(PositionalBufferedStream) version to see header lines in the decode functions. Necessary for binary codecs but a nice side benefit for ascii codecs as well -- Cleaned up the IndexFactory interface so there's a truly general createIndex function that takes the enumerated index type. Added a writeIndex() function that writes an index to disk. -- Vastly expanded the index unit tests and reader tests to really test linear, interval, and tabix indexed files. Updated test.bed, and created a tabix version of it as well. -- Significant BinaryFeaturesTest suite. -- Some test files have indent changes
2012-05-03 19:02:28 +08:00
// TODO -- update for new Tribble interface
// try {
// InputStream is = new ByteArrayInputStream(INPUT_STRING.getBytes());
// AsciiLineReader lineReader = new AsciiLineReader(is);
// codec.readHeader(lineReader);
//
// int counter = 0;
// while (counter++ < linesToRead ) {
// String line = lineReader.readLine();
// if ( line == null )
// break;
//
// T vc = codec.decode(line);
// func.run(vc);
// }
// } catch (Exception e) {
// System.out.println("Benchmarking run failure because of " + e.getMessage());
// }
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
}
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
public void timeV14(int rep) {
for ( int i = 0; i < rep; i++ ) {
FunctionToBenchmark<VariantContext> func = getV14FunctionToBenchmark();
FeatureCodec<VariantContext> codec = new VCFCodec();
runBenchmark(codec, func);
}
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
}
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
public FunctionToBenchmark<VariantContext> getV14FunctionToBenchmark() {
switch ( operation ) {
case READ:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
; // empty operation
}
};
case SUBSET_TO_SAMPLES:
return new FunctionToBenchmark<VariantContext>() {
Set<String> samples;
public void run(final VariantContext vc) {
if ( samples == null )
samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
Bugfix for incorrect allele counting in IndelSummary -- Previous version would count all alt alleles as present in a sample, even if only 1 were present, because of the way VariantEval subsetted VCs -- Updated code for subsetting VCs by sample to be clearer about how it handles rederiving alleles -- Update a few pieces of code to get previous correct behavior -- Updated a few MD5s as now ref calls at sites in dbSNP are counted as having a comp sites, and therefore show up in known sites when Novelty strat is on (which I think is correct) -- Walkers that used old subsetting function with true are now using clearer version that does rederive alleles by default
2012-08-01 23:57:16 +08:00
VariantContext sub = vc.subContextFromSamples(samples);
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
sub.getNSamples();
}
};
case GET_TYPE:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
vc.getType();
}
};
case GET_ID:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
vc.getID();
}
};
case GET_GENOTYPES:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
vc.getGenotypes().size();
}
};
case GET_GENOTYPES_FOR_SAMPLES:
return new FunctionToBenchmark<VariantContext>() {
Set<String> samples;
public void run(final VariantContext vc) {
if ( samples == null )
samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
vc.getGenotypes(samples).size();
}
};
case GET_ATTRIBUTE_STRING:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
vc.getAttribute("AN", null);
}
};
case GET_ATTRIBUTE_INT:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
vc.getAttributeAsInt("AC", 0);
}
};
case GET_N_SAMPLES:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
vc.getNSamples();
}
};
case GET_GENOTYPES_IN_ORDER_OF_NAME:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
; // TODO - TEST IS BROKEN
// int n = 0;
UnitTests for VariantContext for chrCount, getSampleNames, Order function -- Major change to how chromosomeCounts is computed. Now NO_CALL alleles are always excluded. So ChromosomeCounts(A/.) is 1, the previous result would have been 2. -- Naming changes for getSamplesNameInOrder()
2011-11-18 09:37:22 +08:00
// for ( final Genotype g: vc.getGenotypesOrderedByName() ) n++;
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
}
};
case CALC_GENOTYPE_COUNTS:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
vc.getHetCount();
}
};
case MERGE:
return new FunctionToBenchmark<VariantContext>() {
public void run(final VariantContext vc) {
List<VariantContext> toMerge = new ArrayList<VariantContext>();
for ( int i = 0; i < dupsToMerge; i++ ) {
GenotypeCollection renamed to GenotypesContext
2011-11-17 05:24:05 +08:00
GenotypesContext gc = GenotypesContext.create(vc.getNSamples());
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
for ( final Genotype g : vc.getGenotypes() ) {
Efficient Genotype object Intermediate commit -- Created a new Genotype interface with a more limited set of operations -- Old genotype object is now SlowGenotype. New genotype object is FastGenotype. They can be used interchangable -- There's no way to create Genotypes directly any longer. You have to use GenotypeBuilder just like VariantContextBuilder -- Modified lots and lots of code to use GenotypeBuilder -- Added a temporary hidden argument to engine to use FastGenotype by default. Current default is SlowGenotype -- Lots of bug fixes to BCF2 codec and encoder. -- Feature additions -- Now properly handles BCF2 -> BCF2 without decoding or encoding from scratch the BCF2 genotype bytes -- Cleaned up semantics of subContextFromSamples. There's one function that either rederives or not the alleles from the subsetted genotypes -- MASSIVE BUGFIX in SelectVariants. The code has been decoding genotypes always, even if you were not subsetting down samples. Fixed!
2012-06-02 07:25:11 +08:00
gc.add(new GenotypeBuilder(g).name(g.getSampleName()+"_"+i).make());
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
}
First version of VariantContextBuilder
2011-11-19 00:06:15 +08:00
toMerge.add(new VariantContextBuilder(vc).genotypes(gc).make());
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
}
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
VariantContextUtils.simpleMerge(toMerge, null,
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.UNSORTED,
true, false, "set", false, true);
}
};
default: throw new IllegalArgumentException("Unexpected operation " + operation);
}
}
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// --------------------------------------------------------------------------------
//
// V13
//
// In order to use this, you must move the v13 version from archive and uncomment
//
// git mv private/archive/java/src/org/broadinstitute/sting/utils/variantcontext/v13 public/java/test/org/broadinstitute/sting/utils/variantcontext/v13
//
// --------------------------------------------------------------------------------
// public void timeV13(int rep) {
// for ( int i = 0; i < rep; i++ ) {
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext> func = getV13FunctionToBenchmark();
// FeatureCodec<org.broadinstitute.variant.variantcontext.v13.VariantContext> codec = new org.broadinstitute.variant.variantcontext.v13.VCFCodec();
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// runBenchmark(codec, func);
// }
// }
//
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// public FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext> getV13FunctionToBenchmark() {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// switch ( operation ) {
// case READ:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// ; // empty operation
// }
// };
// case SUBSET_TO_SAMPLES:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// List<String> samples;
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// if ( samples == null )
// samples = new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake);
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// org.broadinstitute.variant.variantcontext.v13.VariantContext sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values());
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// sub.getNSamples();
// }
// };
//
// case GET_TYPE:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// vc.getType();
// }
// };
// case GET_ID:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// vc.getID();
// }
// };
// case GET_GENOTYPES:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// vc.getGenotypes().size();
// }
// };
//
// case GET_GENOTYPES_FOR_SAMPLES:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// Set<String> samples;
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// if ( samples == null )
// samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
// vc.getGenotypes(samples).size();
// }
// };
//
// case GET_ATTRIBUTE_STRING:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
Cleanup Genotypes -- Renamed getAttribute to getExtendedAttribute, as this is really what this function does -- Added a few more genotype tests
2012-06-14 02:01:35 +08:00
// vc.getExtendedAttribute("AN", null);
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// }
// };
//
// case GET_ATTRIBUTE_INT:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// vc.getAttributeAsInt("AC", 0);
// }
// };
//
// case GET_N_SAMPLES:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// vc.getNSamples();
// }
// };
//
// case GET_GENOTYPES_IN_ORDER_OF_NAME:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// ; // TODO - TEST IS BROKEN
UnitTests for VariantContext for chrCount, getSampleNames, Order function -- Major change to how chromosomeCounts is computed. Now NO_CALL alleles are always excluded. So ChromosomeCounts(A/.) is 1, the previous result would have been 2. -- Naming changes for getSamplesNameInOrder()
2011-11-18 09:37:22 +08:00
// //vc.getGenotypesOrderedByName();
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// }
// };
//
// case CALC_GENOTYPE_COUNTS:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// vc.getHetCount();
// }
// };
//
// case MERGE:
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
// public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
// List<org.broadinstitute.variant.variantcontext.v13.VariantContext> toMerge = new ArrayList<org.broadinstitute.variant.variantcontext.v13.VariantContext>();
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
//
// for ( int i = 0; i < dupsToMerge; i++ ) {
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// Map<String, org.broadinstitute.variant.variantcontext.v13.Genotype> gc = new HashMap<String, org.broadinstitute.variant.variantcontext.v13.Genotype>();
// for ( final org.broadinstitute.variant.variantcontext.v13.Genotype g : vc.getGenotypes().values() ) {
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// String name = g.getSampleName()+"_"+i;
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// gc.put(name, new org.broadinstitute.variant.variantcontext.v13.Genotype(name,
Change interface to getNegLog10PError to getLog10PError
2011-11-19 10:07:30 +08:00
// g.getAlleles(), g.getLog10PError(), g.getFilters(), g.getAttributes(), g.isPhased(), g.getLikelihoods().getAsVector()));
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// toMerge.add(org.broadinstitute.variant.variantcontext.v13.VariantContext.modifyGenotypes(vc, gc));
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// }
// }
//
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.simpleMerge(b37GenomeLocParser,
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// toMerge, null,
Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.
2012-12-19 03:56:48 +08:00
// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
// org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.GenotypeMergeType.UNSORTED,
V13 version in archive. Can you pulled out wholesale for performance testing
2011-11-17 05:08:46 +08:00
// true, false, "set", false, true);
// }
// };
//
// default: throw new IllegalArgumentException("Unexpected operation " + operation);
// }
// }
More general handling of parameters for VariantContextBenchmark
2011-11-11 23:22:19 +08:00
Expanded, contrastive VariantContextBenchmark -- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4 -- 1.3 VC and associated utilities copied wholesale into test directory under v13
2011-11-17 02:35:16 +08:00
public static void main(String[] args) {
Updating to latest google caliper code
2013-01-08 10:25:44 +08:00
com.google.caliper.Runner.main(VariantContextBenchmark.class, args);
First working version of VariantContextBenchmark
2011-11-11 22:56:00 +08:00
}
}