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Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4774 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-12-02 18:43:24 +00:00
parent 670ae814b3
commit e5282742f9
2 changed files with 19 additions and 20 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
View File

@ -71,10 +71,9 @@ import java.util.Map;
*/
@By( DataSource.READS ) // Only look at covered loci, not every loci of the reference file
@WalkerName( "CountCovariates" )
@ReadFilters( {ZeroMappingQualityReadFilter.class} ) // Filter out all reads with zero mapping quality
@Requires( {DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES} ) // This walker requires both -I input.bam and -R reference.fasta
public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.CountedData, CovariateCounterWalker.CountedData> implements TreeReducible<CovariateCounterWalker.CountedData> {
public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.CountedData, CountCovariatesWalker.CountedData> implements TreeReducible<CountCovariatesWalker.CountedData> {
/////////////////////////////
// Constants
@ -286,7 +285,7 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
// Pull out data for this locus for all the input RODs and check if this is a known variant site in any of them
boolean isSNP = false;
for( final VariantContext vc : tracker.getAllVariantContexts(ref, null, context.getLocation(), false, false) ) {
if( vc != null && vc.isSNP() ) {
if( vc != null ) {
isSNP = true;
break;
}

34
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -18,10 +18,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariates1() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "e2ea7507feb66651f52320c5a46433c2" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "b2191ea11f528b9605b727d8a73dd1e1");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "596a9ec9cbc1da70481e45a5a588a41d" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "507dbd3ba6f54e066d04c4d24f59c3ab" );
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "a48d7fe3a0652a8dbc8d23d22f6ebf03" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "abff8828a9f7cf8e8dfca725d0b74e99");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "c7bef65520106dba41b30b6f4481d6bf" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "286ebc7d8245d47e7d11e92e63800fff" );
for ( String parallelism : Arrays.asList("", " -nt 4")) {
for ( Map.Entry<String, String> entry : e.entrySet() ) {
@ -53,10 +53,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibrator1() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "da79dcc74336a6333f75aeb231590436" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "4d24b4683a9b20e93837da75fff2489f");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "b26a07cc3d3f6a607e786ebcc2c9c8ac" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "165e93b7713d099beb5919b595f41321" );
e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "d75197ddba03930c115dbebf869b2b3e" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "66ee21c42dcd1abb8418113decea68eb");
e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "e8bca2fa6b16d2b32b1f3fcb19772b9f" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "f6865fee5bbb9e954aad8f9da97277b4" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -84,7 +84,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesUseOriginalQuals() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "db6c0dca1ec121f8c2e6d20f4969dee5");
e.put( validationDataLocation + "originalQuals.1kg.chr1.1-1K.bam", "3404965ec4fa99873fe6a44521944fd5");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -108,7 +108,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorMaxQ70() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "4d24b4683a9b20e93837da75fff2489f" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "66ee21c42dcd1abb8418113decea68eb" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -139,7 +139,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "013822cfa4f276d48ca99c014c23c124" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "c5b3c25c1c5f02f00a0733c173aea903" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -165,7 +165,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorSolidIndelsRemoveRefBias() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "85c0500f9f4ba0d613a77d34b5c84a64" );
e.put( validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "907ebdc7da8c61fb0141c8441de52844" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -220,7 +220,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesVCFPlusDBsnp() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "949c2ecb24a4189e106d372b05ec725f");
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "370b70fde2808499480118591061bcec");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -248,7 +248,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesNoReadGroups() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "62dab3db2172695cf95fba7f543a4058" );
e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "0e65ee67dcd2fa4a6cca96e0d0bc4a8d" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -278,7 +278,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorNoReadGroups() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "528f8d8812e72296d427af795d94eccc" );
e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "c931a3965d7cb83417b04980314cd6f7" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -307,7 +307,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesNoIndex() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "abc4248cb5f718594a63409a151d679e" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "7952a650ec385cfff5a8314282e097aa" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -333,7 +333,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorNoIndex() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "bd29f127ac19d8eb2108394fa2a889ce" );
e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "199842068feeb4f5a0301b4e71bfe926" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();