Examples with IntegrationTestSpec org.broadinstitute.hellbender.utils.test.IntegrationTestSpec used on opensource projects

Example 61 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class PileupIntegrationTest method testVerbosePileup.

@Test
public void testVerbosePileup() throws IOException {
    // GATK 3.5 code have a the last line with a REDUCE RESULT that was removed in this implementation
    IntegrationTestSpec testSpec = new IntegrationTestSpec(" -L 20:9999990-10000000" + " -verbose " + " -R " + b37_reference_20_21 + " -I " + NA12878_20_21_WGS_bam + " -O %s", Arrays.asList(TEST_OUTPUT_DIRECTORY + "expectedVerbosePileup.txt"));
    testSpec.executeTest("testVerbosePileup", this);
}

Example 62 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ASEReadCounterIntegrationTest method testASEReadCounterWithLowMQ.

@Test
public void testASEReadCounterWithLowMQ() throws Exception {
    IntegrationTestSpec spec = new IntegrationTestSpec("-R " + b37_reference_20_21 + " -I " + largeFileTestDir + "NA12878.RNAseq.bam -V " + aseTestDir + "NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 1 -O %s ", Arrays.asList(aseTestDir + "expected.ASEReadCount.WithLowMQ.table"));
    spec.executeTest("test high mq with no read passing", this);
}

Example 63 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ASEReadCounterIntegrationTest method testASEReadCounterWithLowMQNoDedup.

@Test
public void testASEReadCounterWithLowMQNoDedup() throws Exception {
    IntegrationTestSpec spec = new IntegrationTestSpec("-R " + b37_reference_20_21 + " -I " + largeFileTestDir + "NA12878.RNAseq.bam -V " + aseTestDir + "NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 10 -O %s -DF NotDuplicateReadFilter", Arrays.asList(aseTestDir + "expected.ASEReadCount.WithLowMQNoDedup.table"));
    spec.executeTest("test high mq with no read passing", this);
}

Example 64 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ASEReadCounterIntegrationTest method testASEReadCounterWithHighMQLowBQ.

@Test
public void testASEReadCounterWithHighMQLowBQ() throws Exception {
    IntegrationTestSpec spec = new IntegrationTestSpec("-R " + b37_reference_20_21 + " -I " + largeFileTestDir + "NA12878.RNAseq.bam -V " + aseTestDir + "NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 60 -mbq 10 -O %s ", Arrays.asList(aseTestDir + "expected.ASEReadCount.WithHighMQLowBQ.table"));
    spec.executeTest("test high mq with no read passing", this);
}

Example 65 with IntegrationTestSpec

use of org.broadinstitute.hellbender.utils.test.IntegrationTestSpec in project gatk by broadinstitute.

the class ASEReadCounterIntegrationTest method testASEReadCounterWithCountReads.

@Test
public void testASEReadCounterWithCountReads() throws Exception {
    IntegrationTestSpec spec = new IntegrationTestSpec("-R " + b37_reference_20_21 + " -I " + largeFileTestDir + "NA12878.RNAseq.bam -V " + aseTestDir + "NA12878.chr20_2444518_2637800.RNAseq.SYNONYMOUS_CODING.vcf -mmq 60 -mbq 10 -O %s -overlap COUNT_READS", Arrays.asList(aseTestDir + "expected.ASEReadCount.WithCountReads.table"));
    spec.executeTest("test high mq with no read passing", this);
}