Commit 5a9aa210 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.18.0+dfsg

parent 5c5e2f76

README.md

+2 −5
Original line number Diff line number Diff line
@@ -49,12 +49,9 @@ Example gradle usage from the htsjdk root directory: 
 ```

 ./gradlew test



 ./gradlew test -Dtest.single=TestClassName

 ./gradlew test --tests AlleleUnitTest



 ./gradlew test --tests htsjdk.variant.variantcontext.AlleleUnitTest

 ./gradlew test --tests "*AlleleUnitTest"



 ./gradlew test --tests "*AlleleUnitTest" --debug-jvm

 ./gradlew test --tests AlleleUnitTest --debug-jvm

 ```



- run tests and collect coverage information (report will be in `build/reports/jacoco/test/html/index.html`)

build.gradle

+1 −0
Original line number Diff line number Diff line
@@ -43,6 +43,7 @@ dependencies { 
    testRuntime 'org.pegdown:pegdown:1.6.0' // Necessary for generating HTML reports with ScalaTest

    testCompile "org.testng:testng:6.14.3"

    testCompile "com.google.jimfs:jimfs:1.1"

    testCompile "com.google.guava:guava:26.0-jre"

 }



sourceCompatibility = 1.8

src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java

+2 −2
Original line number Diff line number Diff line
@@ -23,7 +23,7 @@ 
 */

package htsjdk.samtools;



import javax.xml.bind.annotation.XmlTransient;



import java.io.Serializable;

import java.util.LinkedHashMap;

import java.util.Map;
@@ -33,7 +33,7 @@ import java.util.Set; 
 * Base class for the various concrete records in a SAM header, providing uniform

 * access to the attributes.

 */

@XmlTransient /* don't consider this class for XML-serialization */



public abstract class AbstractSAMHeaderRecord implements Serializable {

    public static final long serialVersionUID = 1L;

src/main/java/htsjdk/samtools/BAMRecord.java

+2 −2
Original line number Diff line number Diff line
@@ -310,7 +310,7 @@ public class BAMRecord extends SAMRecord { 
     * extracts the CIGAR from the CG tag and places it into the (in memory) cigar.

     */

    private void extractCigarFromCGAttribute(final Cigar sentinelCigar) throws IllegalStateException {

        final int[] cigarFromCG = (int[]) getAttribute(SAMTagUtil.getSingleton().CG);

        final int[] cigarFromCG = (int[]) getAttribute(SAMTag.CG.getBinaryTag());



        if (cigarFromCG == null) return;
@@ -353,7 +353,7 @@ public class BAMRecord extends SAMRecord { 
        initializeCigar(decodedCigar);



        // remove CG attribute.

        setAttribute(SAMTagUtil.getSingleton().CG, null);

        setAttribute(SAMTag.CG.getBinaryTag(), null);

    }



    /**

src/main/java/htsjdk/samtools/CRAMIterator.java

+7 −8
Original line number Diff line number Diff line
@@ -34,10 +34,7 @@ import htsjdk.samtools.util.Log; 
import java.io.IOException;

import java.io.InputStream;

import java.math.BigInteger;

import java.util.ArrayList;

import java.util.Collections;

import java.util.Iterator;

import java.util.List;

import java.util.*;



import htsjdk.samtools.cram.CRAMException;
@@ -259,9 +256,7 @@ public class CRAMIterator implements SAMRecordIterator { 
        if (!iterator.hasNext()) {

            try {

                nextContainer();

            } catch (IOException e) {

                throw new SAMException(e);

            } catch (IllegalAccessException e) {

            } catch (IOException | IllegalAccessException e) {

                throw new SAMException(e);

            }

        }
@@ -271,7 +266,11 @@ public class CRAMIterator implements SAMRecordIterator { 


    @Override

    public SAMRecord next() {

        if (hasNext()) {

            return iterator.next();

        } else {

            throw new NoSuchElementException();

        }

    }



    @Override