1. Added support for JNI integration for LoglessCaching PairHMM AVX
implementation. 2. Contains lots of debug code 3. Only invokes JNI for subComputeReadLikelihoodGivenHaplotypeLog10
This commit is contained in:
Karthik Gururaj
parent
f6a44afa3a
commit
e8a5022777
14
build.xml
14
build.xml
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@ -270,18 +270,18 @@
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<mkdir dir="${lib.dir}"/>
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<mkdir dir="${ivy.jar.dir}"/>
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<!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
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<!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
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<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
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dest="${ivy.jar.dir}/${ivy.jar.file}"
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usetimestamp="true"/>
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<!--<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"-->
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<!--dest="${ivy.jar.dir}/${ivy.jar.file}"-->
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<!--usetimestamp="true"/>-->
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<taskdef resource="org/apache/ivy/ant/antlib.xml"
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uri="antlib:org.apache.ivy.ant"
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classpath="${ivy.jar.dir}/${ivy.jar.file}"/>
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<get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}"
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dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"
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usetimestamp="true"/>
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<!--<get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}"-->
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<!--dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"-->
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<!--usetimestamp="true"/>-->
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<taskdef resource="org/apache/maven/artifact/ant/antlib.xml"
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uri="antlib:antlib:org.apache.maven.artifact.ant"
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classpath="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"/>
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@ -81,25 +81,28 @@ public class PairHMMLikelihoodCalculationEngine implements LikelihoodCalculation
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private final boolean noFpga;
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private final ThreadLocal<PairHMM> pairHMMThreadLocal = new ThreadLocal<PairHMM>() {
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@Override
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protected PairHMM initialValue() {
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switch (hmmType) {
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case EXACT: return new Log10PairHMM(true);
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case ORIGINAL: return new Log10PairHMM(false);
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case LOGLESS_CACHING:
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if (noFpga || !CnyPairHMM.isAvailable())
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return new LoglessPairHMM();
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else
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return new CnyPairHMM();
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case ARRAY_LOGLESS:
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if (noFpga || !CnyPairHMM.isAvailable())
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return new ArrayLoglessPairHMM();
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else
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return new CnyPairHMM();
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default:
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throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, and ARRAY_LOGLESS.");
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}
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}
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@Override
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protected PairHMM initialValue() {
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switch (hmmType) {
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case EXACT: return new Log10PairHMM(true);
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case ORIGINAL: return new Log10PairHMM(false);
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case LOGLESS_CACHING:
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if (noFpga || !CnyPairHMM.isAvailable())
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{
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//return new LoglessPairHMM();
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return new JNILoglessPairHMM();
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}
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else
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return new CnyPairHMM();
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case ARRAY_LOGLESS:
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if (noFpga || !CnyPairHMM.isAvailable())
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return new ArrayLoglessPairHMM();
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else
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return new CnyPairHMM();
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default:
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throw new UserException.BadArgumentValue("pairHMM", "Specified pairHMM implementation is unrecognized or incompatible with the HaplotypeCaller. Acceptable options are ORIGINAL, EXACT, CACHING, LOGLESS_CACHING, and ARRAY_LOGLESS.");
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}
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}
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};
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// Attempted to do as below, to avoid calling pairHMMThreadLocal.get() later on, but it resulted in a NullPointerException
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// private final PairHMM pairHMM = pairHMMThreadLocal.get();
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@ -0,0 +1,382 @@
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/*
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* By downloading the PROGRAM you agree to the following terms of use:
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*
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* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
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*
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* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
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*
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* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
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* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
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* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
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*
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* 1. DEFINITIONS
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* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
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*
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* 2. LICENSE
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* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
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* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
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* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
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* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
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*
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* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
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* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
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* Copyright 2012 Broad Institute, Inc.
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* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
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* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
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*
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* 4. INDEMNIFICATION
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* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
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*
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* 5. NO REPRESENTATIONS OR WARRANTIES
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* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
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* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
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*
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* 6. ASSIGNMENT
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* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
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*
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* 7. MISCELLANEOUS
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* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
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* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
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* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
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* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
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* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
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* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
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* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
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*/
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package org.broadinstitute.sting.utils.pairhmm;
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import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.sting.utils.haplotype.Haplotype;
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import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
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import org.broadinstitute.variant.variantcontext.Allele;
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import java.util.List;
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import java.util.Map;
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/**
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* Created with IntelliJ IDEA.
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* User: rpoplin, carneiro
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* Date: 10/16/12
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*/
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public class JNILoglessPairHMM extends LoglessPairHMM {
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static {
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System.loadLibrary("JNILoglessPairHMM");
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}
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private static final boolean debug = true; //simulates ifdef
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private static final boolean debug2 = false;
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private static final boolean debug3 = false;
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@Override
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protected void finalize() throws Throwable {
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try{
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debugClose();
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}catch(Throwable t){
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throw t;
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}finally{
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super.finalize();
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}
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}
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private native void jniInitialize(final int readMaxLength, final int haplotypeMaxLength);
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private native static void jniInitializeProbabilities(final double[][] transition, final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP);
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private native double jniInitializePriorsAndUpdateCells(
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boolean doInitialization,
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final int paddedReadLength, final int paddedHaplotypeLength,
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final byte[] readBases, final byte[] haplotypeBases, final byte[] readQuals,
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final int hapStartIndex);
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private native double jniSubComputeReadLikelihoodGivenHaplotypeLog10(
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final int readLength, final int haplotypeLength,
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final byte[] readBases, final byte[] haplotypeBases, final byte[] readQuals,
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final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP,
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final int hapStartIndex);
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/**
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* {@inheritDoc}
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*/
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@Override
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public void initialize(final int readMaxLength, final int haplotypeMaxLength)
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{
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super.initialize(readMaxLength, haplotypeMaxLength);
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if(debug3)
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{
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System.out.println("Java: alloc initialized readMaxLength : "+readMaxLength+" haplotypeMaxLength : "+haplotypeMaxLength);
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debugDump("lengths_java.txt", String.format("%d %d\n",readMaxLength, haplotypeMaxLength),
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true);
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}
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if(debug2)
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jniInitialize(readMaxLength, haplotypeMaxLength);
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public PerReadAlleleLikelihoodMap computeLikelihoods(final List<GATKSAMRecord> reads, final Map<Allele, Haplotype> alleleHaplotypeMap, final Map<GATKSAMRecord, byte[]> GCPArrayMap)
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{
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PerReadAlleleLikelihoodMap retValue = super.computeLikelihoods(reads, alleleHaplotypeMap, GCPArrayMap);
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if(debug)
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debugClose();
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return retValue;
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}
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//{
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//// (re)initialize the pairHMM only if necessary
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//final int readMaxLength = findMaxReadLength(reads);
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//final int haplotypeMaxLength = findMaxHaplotypeLength(alleleHaplotypeMap);
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//if (!initialized || readMaxLength > maxReadLength || haplotypeMaxLength > maxHaplotypeLength)
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//{ initialize(readMaxLength, haplotypeMaxLength); }
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//if ( ! initialized )
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//throw new IllegalStateException("Must call initialize before calling computeReadLikelihoodGivenHaplotypeLog10");
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//final PerReadAlleleLikelihoodMap likelihoodMap = new PerReadAlleleLikelihoodMap();
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//for(GATKSAMRecord read : reads){
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//final byte[] readBases = read.getReadBases();
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//final byte[] readQuals = read.getBaseQualities();
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//final byte[] readInsQuals = read.getBaseInsertionQualities();
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//final byte[] readDelQuals = read.getBaseDeletionQualities();
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//final byte[] overallGCP = GCPArrayMap.get(read);
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//// peak at the next haplotype in the list (necessary to get nextHaplotypeBases, which is required for caching in the array implementation)
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//byte[] currentHaplotypeBases = null;
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//boolean isFirstHaplotype = true;
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//Allele currentAllele = null;
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//double log10l;
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//for (final Allele allele : alleleHaplotypeMap.keySet()){
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//final Haplotype haplotype = alleleHaplotypeMap.get(allele);
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//final byte[] nextHaplotypeBases = haplotype.getBases();
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//if (currentHaplotypeBases != null) {
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//log10l = computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases,
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//readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype, nextHaplotypeBases);
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//likelihoodMap.add(read, currentAllele, log10l);
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//}
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//// update the current haplotype
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//currentHaplotypeBases = nextHaplotypeBases;
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//currentAllele = allele;
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//}
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//// process the final haplotype
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//if (currentHaplotypeBases != null) {
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//// there is no next haplotype, so pass null for nextHaplotypeBases.
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//log10l = computeReadLikelihoodGivenHaplotypeLog10(currentHaplotypeBases,
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//readBases, readQuals, readInsQuals, readDelQuals, overallGCP, isFirstHaplotype, null);
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//likelihoodMap.add(read, currentAllele, log10l);
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//}
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//}
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//return likelihoodMap;
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//}
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///**
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//* {@inheritDoc}
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//*/
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//@Override
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//protected final double computeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,
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//final byte[] readBases,
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//final byte[] readQuals,
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//final byte[] insertionGOP,
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//final byte[] deletionGOP,
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//final byte[] overallGCP,
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//final boolean recacheReadValues,
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//final byte[] nextHaploytpeBases) {
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//if ( haplotypeBases == null ) throw new IllegalArgumentException("haplotypeBases cannot be null");
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//if ( haplotypeBases.length > maxHaplotypeLength ) throw new IllegalArgumentException("Haplotype bases is too long, got " + haplotypeBases.length + " but max is " + maxHaplotypeLength);
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//if ( readBases == null ) throw new IllegalArgumentException("readBases cannot be null");
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//if ( readBases.length > maxReadLength ) throw new IllegalArgumentException("readBases is too long, got " + readBases.length + " but max is " + maxReadLength);
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//if ( readQuals.length != readBases.length ) throw new IllegalArgumentException("Read bases and read quals aren't the same size: " + readBases.length + " vs " + readQuals.length);
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//if ( insertionGOP.length != readBases.length ) throw new IllegalArgumentException("Read bases and read insertion quals aren't the same size: " + readBases.length + " vs " + insertionGOP.length);
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//if ( deletionGOP.length != readBases.length ) throw new IllegalArgumentException("Read bases and read deletion quals aren't the same size: " + readBases.length + " vs " + deletionGOP.length);
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//if ( overallGCP.length != readBases.length ) throw new IllegalArgumentException("Read bases and overall GCP aren't the same size: " + readBases.length + " vs " + overallGCP.length);
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//paddedReadLength = readBases.length + 1;
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//paddedHaplotypeLength = haplotypeBases.length + 1;
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//double result = subComputeReadLikelihoodGivenHaplotypeLog10(haplotypeBases, readBases, readQuals, insertionGOP, deletionGOP, overallGCP, 0, true, 0);
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//if ( ! MathUtils.goodLog10Probability(result) )
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//throw new IllegalStateException("PairHMM Log Probability cannot be greater than 0: " + String.format("haplotype: %s, read: %s, result: %f", Arrays.toString(haplotypeBases), Arrays.toString(readBases), result));
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//// Warning: Careful if using the PairHMM in parallel! (this update has to be taken care of).
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//// Warning: This assumes no downstream modification of the haplotype bases (saves us from copying the array). It is okay for the haplotype caller and the Unified Genotyper.
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//// KG: seems pointless is not being used anywhere
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//previousHaplotypeBases = haplotypeBases;
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//return result;
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//}
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/**
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* {@inheritDoc}
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*/
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@Override
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public double subComputeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,
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final byte[] readBases,
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final byte[] readQuals,
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final byte[] insertionGOP,
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final byte[] deletionGOP,
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final byte[] overallGCP,
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final int hapStartIndex,
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final boolean recacheReadValues,
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final int nextHapStartIndex) {
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//System.out.println("#### START STACK TRACE ####");
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//for (StackTraceElement ste : Thread.currentThread().getStackTrace()) {
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//System.out.println(ste);
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//}
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//System.out.println("#### END STACK TRACE ####");
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//
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jniSubComputeReadLikelihoodGivenHaplotypeLog10(readBases.length, haplotypeBases.length,
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readBases, haplotypeBases, readQuals,
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insertionGOP, deletionGOP, overallGCP,
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hapStartIndex);
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boolean doInitialization = (previousHaplotypeBases == null || previousHaplotypeBases.length != haplotypeBases.length);
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if (doInitialization) {
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final double initialValue = INITIAL_CONDITION / haplotypeBases.length;
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// set the initial value (free deletions in the beginning) for the first row in the deletion matrix
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for( int j = 0; j < paddedHaplotypeLength; j++ ) {
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deletionMatrix[0][j] = initialValue;
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}
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}
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if ( ! constantsAreInitialized || recacheReadValues ) {
|
||||
initializeProbabilities(transition, insertionGOP, deletionGOP, overallGCP);
|
||||
if(debug3)
|
||||
{
|
||||
System.out.println("Java: initializeProbabilities lengths : "+insertionGOP.length+" padded "+paddedReadLength+" "+paddedHaplotypeLength);
|
||||
for(int i=0;i<insertionGOP.length;++i)
|
||||
for(int j=0;j<6;++j)
|
||||
debugDump("transitions_java.txt",String.format("%e\n",transition[i+1][j]),true);
|
||||
}
|
||||
if(debug2)
|
||||
jniInitializeProbabilities(transition, insertionGOP, deletionGOP, overallGCP);
|
||||
|
||||
// note that we initialized the constants
|
||||
constantsAreInitialized = true;
|
||||
}
|
||||
|
||||
if(debug3)
|
||||
System.out.println("Java: initializePriors : lengths "+readBases.length+" "+haplotypeBases.length+" padded "+paddedReadLength+" "+paddedHaplotypeLength + " doNotUseTristateCorrection "+doNotUseTristateCorrection);
|
||||
initializePriors(haplotypeBases, readBases, readQuals, hapStartIndex);
|
||||
|
||||
for (int i = 1; i < paddedReadLength; i++) {
|
||||
// +1 here is because hapStartIndex is 0-based, but our matrices are 1 based
|
||||
for (int j = hapStartIndex+1; j < paddedHaplotypeLength; j++) {
|
||||
updateCell(i, j, prior[i][j], transition[i]);
|
||||
}
|
||||
}
|
||||
|
||||
// final probability is the log10 sum of the last element in the Match and Insertion state arrays
|
||||
// this way we ignore all paths that ended in deletions! (huge)
|
||||
// but we have to sum all the paths ending in the M and I matrices, because they're no longer extended.
|
||||
final int endI = paddedReadLength - 1;
|
||||
double finalSumProbabilities = 0.0;
|
||||
for (int j = 1; j < paddedHaplotypeLength; j++) {
|
||||
finalSumProbabilities += matchMatrix[endI][j] + insertionMatrix[endI][j];
|
||||
}
|
||||
if(debug2)
|
||||
jniInitializePriorsAndUpdateCells(doInitialization, paddedReadLength, paddedHaplotypeLength,
|
||||
readBases, haplotypeBases, readQuals,
|
||||
hapStartIndex);
|
||||
if(debug)
|
||||
debugDump("return_values_java.txt",String.format("%e\n",Math.log10(finalSumProbabilities) - INITIAL_CONDITION_LOG10),true);
|
||||
++numCalls;
|
||||
//if(numCalls == 100)
|
||||
//{
|
||||
//debugClose();
|
||||
//System.exit(0);
|
||||
//}
|
||||
return Math.log10(finalSumProbabilities) - INITIAL_CONDITION_LOG10;
|
||||
}
|
||||
|
||||
/**
|
||||
* Initializes the matrix that holds all the constants related to the editing
|
||||
* distance between the read and the haplotype.
|
||||
*
|
||||
* @param haplotypeBases the bases of the haplotype
|
||||
* @param readBases the bases of the read
|
||||
* @param readQuals the base quality scores of the read
|
||||
* @param startIndex where to start updating the distanceMatrix (in case this read is similar to the previous read)
|
||||
*/
|
||||
protected void initializePriors(final byte[] haplotypeBases, final byte[] readBases, final byte[] readQuals, final int startIndex) {
|
||||
|
||||
// initialize the pBaseReadLog10 matrix for all combinations of read x haplotype bases
|
||||
// Abusing the fact that java initializes arrays with 0.0, so no need to fill in rows and columns below 2.
|
||||
|
||||
for (int i = 0; i < readBases.length; i++) {
|
||||
final byte x = readBases[i];
|
||||
final byte qual = readQuals[i];
|
||||
for (int j = startIndex; j < haplotypeBases.length; j++) {
|
||||
final byte y = haplotypeBases[j];
|
||||
prior[i+1][j+1] = ( x == y || x == (byte) 'N' || y == (byte) 'N' ?
|
||||
QualityUtils.qualToProb(qual) : (QualityUtils.qualToErrorProb(qual) / (doNotUseTristateCorrection ? 1.0 : TRISTATE_CORRECTION)) );
|
||||
if(debug3)
|
||||
debugDump("priors_java.txt",String.format("%e\n",prior[i+1][j+1]),true);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Initializes the matrix that holds all the constants related to quality scores.
|
||||
*
|
||||
* @param insertionGOP insertion quality scores of the read
|
||||
* @param deletionGOP deletion quality scores of the read
|
||||
* @param overallGCP overall gap continuation penalty
|
||||
*/
|
||||
@Requires({
|
||||
"insertionGOP != null",
|
||||
"deletionGOP != null",
|
||||
"overallGCP != null"
|
||||
})
|
||||
@Ensures("constantsAreInitialized")
|
||||
protected static void initializeProbabilities(final double[][] transition, final byte[] insertionGOP, final byte[] deletionGOP, final byte[] overallGCP) {
|
||||
for (int i = 0; i < insertionGOP.length; i++) {
|
||||
final int qualIndexGOP = Math.min(insertionGOP[i] + deletionGOP[i], Byte.MAX_VALUE);
|
||||
transition[i+1][matchToMatch] = QualityUtils.qualToProb((byte) qualIndexGOP);
|
||||
transition[i+1][indelToMatch] = QualityUtils.qualToProb(overallGCP[i]);
|
||||
transition[i+1][matchToInsertion] = QualityUtils.qualToErrorProb(insertionGOP[i]);
|
||||
transition[i+1][insertionToInsertion] = QualityUtils.qualToErrorProb(overallGCP[i]);
|
||||
transition[i+1][matchToDeletion] = QualityUtils.qualToErrorProb(deletionGOP[i]);
|
||||
transition[i+1][deletionToDeletion] = QualityUtils.qualToErrorProb(overallGCP[i]);
|
||||
|
||||
//TODO it seems that it is not always the case that matchToMatch + matchToDeletion + matchToInsertion == 1.
|
||||
//TODO We have detected cases of 1.00002 which can cause problems downstream. This are typically masked
|
||||
//TODO by the fact that we always add a indelToMatch penalty to all PairHMM likelihoods (~ -0.1)
|
||||
//TODO This is in fact not well justified and although it does not have any effect (since is equally added to all
|
||||
//TODO haplotypes likelihoods) perhaps we should just remove it eventually and fix this != 1.0 issue here.
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Updates a cell in the HMM matrix
|
||||
*
|
||||
* The read and haplotype indices are offset by one because the state arrays have an extra column to hold the
|
||||
* initial conditions
|
||||
|
||||
* @param indI row index in the matrices to update
|
||||
* @param indJ column index in the matrices to update
|
||||
* @param prior the likelihood editing distance matrix for the read x haplotype
|
||||
* @param transition an array with the six transition relevant to this location
|
||||
*/
|
||||
protected void updateCell( final int indI, final int indJ, final double prior, final double[] transition) {
|
||||
|
||||
matchMatrix[indI][indJ] = prior * ( matchMatrix[indI - 1][indJ - 1] * transition[matchToMatch] +
|
||||
insertionMatrix[indI - 1][indJ - 1] * transition[indelToMatch] +
|
||||
deletionMatrix[indI - 1][indJ - 1] * transition[indelToMatch] );
|
||||
insertionMatrix[indI][indJ] = matchMatrix[indI - 1][indJ] * transition[matchToInsertion] + insertionMatrix[indI - 1][indJ] * transition[insertionToInsertion];
|
||||
deletionMatrix[indI][indJ] = matchMatrix[indI][indJ - 1] * transition[matchToDeletion] + deletionMatrix[indI][indJ - 1] * transition[deletionToDeletion];
|
||||
if(debug3)
|
||||
{
|
||||
debugDump("matrices_java.txt",String.format("%e\n",matchMatrix[indI][indJ]),true);
|
||||
debugDump("matrices_java.txt",String.format("%e\n",insertionMatrix[indI][indJ]),true);
|
||||
debugDump("matrices_java.txt",String.format("%e\n",deletionMatrix[indI][indJ]),true);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -50,6 +50,13 @@ import com.google.java.contract.Ensures;
|
|||
import com.google.java.contract.Requires;
|
||||
import org.broadinstitute.sting.utils.QualityUtils;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.FileWriter;
|
||||
import java.io.BufferedWriter;
|
||||
import java.util.Map;
|
||||
import java.util.HashMap;
|
||||
import java.io.IOException;
|
||||
|
||||
/**
|
||||
* Created with IntelliJ IDEA.
|
||||
* User: rpoplin, carneiro
|
||||
|
|
@ -69,7 +76,48 @@ public class LoglessPairHMM extends N2MemoryPairHMM {
|
|||
protected static final int matchToDeletion = 4;
|
||||
protected static final int deletionToDeletion = 5;
|
||||
|
||||
protected static int numCalls = 0;
|
||||
protected HashMap<String, BufferedWriter> filenameToWriter = new HashMap<String, BufferedWriter>();
|
||||
protected void debugDump(String filename, String s, boolean toAppend)
|
||||
{
|
||||
try
|
||||
{
|
||||
File file = new File(filename);
|
||||
if (!file.exists())
|
||||
file.createNewFile();
|
||||
BufferedWriter currWriter = filenameToWriter.get(filename);
|
||||
if(currWriter == null)
|
||||
{
|
||||
FileWriter fw = new FileWriter(file, toAppend);
|
||||
currWriter = new BufferedWriter(fw);
|
||||
filenameToWriter.put(filename, currWriter);
|
||||
}
|
||||
currWriter.write(s);
|
||||
}
|
||||
catch(IOException e)
|
||||
{
|
||||
e.printStackTrace();
|
||||
}
|
||||
}
|
||||
|
||||
protected void debugClose()
|
||||
{
|
||||
for(Map.Entry<String, BufferedWriter> currEntry : filenameToWriter.entrySet())
|
||||
{
|
||||
BufferedWriter currWriter = currEntry.getValue();
|
||||
try
|
||||
{
|
||||
currWriter.flush();
|
||||
currWriter.close();
|
||||
}
|
||||
catch(IOException e)
|
||||
{
|
||||
e.printStackTrace();
|
||||
|
||||
}
|
||||
}
|
||||
filenameToWriter.clear();
|
||||
}
|
||||
/**
|
||||
* {@inheritDoc}
|
||||
*/
|
||||
|
|
|
|||
Loading…
Reference in New Issue