zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Very basic intergration tests for ReducedReads, to allow safe optimization of the code 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5970 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-06-09 17:06:32 +00:00
parent 895e86c544
commit ac3620839c
1 changed files with 36 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

36
java/test/org/broadinstitute/sting/playground/gatk/walkers/reducereads/ReduceReadsIntegrationTest.java 100755
View File

@ -0,0 +1,36 @@
package org.broadinstitute.sting.playground.gatk.walkers.reducereads;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.Arrays;
public class ReduceReadsIntegrationTest extends WalkerTest {
final static String REF = b37KGReference;
final String BAM = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
final String L = "20:10,100,000-10,200,000";
private void RRTest(String args, String md5) {
String base = String.format("-T ReduceReads -R %s -I %s -L %s", REF, BAM, L) + " -o %s";
WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5));
executeTest("testReduceReads1: args=" + args, spec);
}
@Test()
public void testReduceReadsBase() {
RRTest("", "6c34409f19ba2e5b21f3bfe6847dadda");
}
@Test()
public void testReduceReads50MaxReads() {
RRTest(" -mravs 50", "3a896ac6e2ea0fc0a3fb4348d31313b6");
}
@Test()
public void testReduceReadsMinBasesForConsensus10000() {
RRTest(" -mbrc 10000", "d8edbc04fd47cd1d64f2ce08459f7dae");
}
}