Commit 44e11d1b authored by Dmitry Smirnov's avatar Dmitry Smirnov

SQ RN * excluded from reference check

parent d4de8fb6
Pipeline #45083 passed with stages
in 3 minutes and 5 seconds
......@@ -20,7 +20,7 @@ wrapper{
group = 'uk.ac.ebi.ena'
ext.version_base = '1.1.10'
ext.version_base = '1.1.11'
version = version_base
sourceCompatibility = '1.8'
targetCompatibility = '1.8'
......
......@@ -4,7 +4,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>uk.ac.ebi.ena</groupId>
<artifactId>readtools</artifactId>
<version>1.1.10</version>
<version>1.1.11</version>
<inceptionYear>2019</inceptionYear>
<licenses>
<license>
......
......@@ -224,6 +224,9 @@ CramReferenceInfo
es.prestartAllCoreThreads();
for( SAMSequenceRecord sequenceRecord : reader.getFileHeader().getSequenceDictionary().getSequences() )
{
if( "*".equals( sequenceRecord.getSequenceName() ) )
continue;
es.getQueue().put(() -> {
count.incrementAndGet();
String md5 = sequenceRecord.getAttribute( SAMSequenceRecord.MD5_TAG );
......
package uk.ac.ebi.ena.readtools.webin.cli.rawreads.refs;
import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.net.URLDecoder;
import java.util.Map;
import org.junit.Assert;
import org.junit.Test;
import uk.ac.ebi.ena.readtools.webin.cli.rawreads.BamScannerTest;
public class
CramReferenceInfoTest
{
@Test public void
testUnalignedCram() throws IOException
{
URL url = BamScannerTest.class.getClassLoader().getResource( "uk/ac/ebi/ena/webin/cli/rawreads/nc-RNAs_DKC1_WT_1_1st_read.cram" );
File file = new File( URLDecoder.decode( url.getFile(), "UTF-8" ) );
CramReferenceInfo cri = new CramReferenceInfo();
Map<?,?> result = cri.confirmFileReferences( file );
Assert.assertEquals( 0, result.size() );
}
@Test public void
testCorrectCramHeader() throws IOException
{
URL url = BamScannerTest.class.getClassLoader().getResource( "uk/ac/ebi/ena/webin/cli/rawreads/15194_1#135.cram" );
File file = new File( URLDecoder.decode( url.getFile(), "UTF-8" ) );
CramReferenceInfo cri = new CramReferenceInfo();
Map<?,?> result = cri.confirmFileReferences( file );
Assert.assertEquals( 66, result.size() );
}
}
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