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Minor change to solid warning message. Added note for a future solid recalibration integration test when we get the required data file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2590 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-15 16:31:25 +00:00
parent 70df30fc1b
commit df998041a8
2 changed files with 11 additions and 6 deletions
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14
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
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@ -57,7 +57,7 @@ public class RecalDataManager {
private static boolean warnUserNullReadGroup = false;
private static boolean warnUserNoColorSpace = false;
public static final String versionString = "v2.2.10"; // Major version, minor version, and build number
public static final String versionString = "v2.2.11"; // Major version, minor version, and build number
RecalDataManager() {
data = new NestedHashMap();
@ -251,6 +251,7 @@ public class RecalDataManager {
* @param read The SAMRecord to parse
*/
public static void parseColorSpace( final SAMRecord read ) {
// If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base
if( read.getReadGroup().getPlatform().equalsIgnoreCase("SOLID") ) {
if( read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null ) { // Haven't calculated the inconsistency array yet for this read
@ -279,8 +280,8 @@ public class RecalDataManager {
read.setAttribute( RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency );
} else if ( !warnUserNoColorSpace ) { // Warn the user if we can't find the color space tag
Utils.warnUser("Unable to find color space information in SOLID read. First observed at read with name = " + read.getReadName());
Utils.warnUser("This calculation is critically dependent on being able to know when reference bases were inserted into the SOLID read. Are you sure you want to proceed?");
Utils.warnUser("Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName());
Utils.warnUser("This calculation is critically dependent on being able to know when reference bases were inserted into SOLiD reads. Are you sure you want to proceed?");
warnUserNoColorSpace = true;
}
}
@ -337,14 +338,14 @@ public class RecalDataManager {
}
} else if ( !warnUserNoColorSpace ) { // Warn the user if we can't find the color space tag
Utils.warnUser("Unable to find color space information in SOLID read. First observed at read with name = " + read.getReadName());
Utils.warnUser("This calculation is critically dependent on being able to know when reference bases were inserted into the SOLID read. Are you sure you want to proceed?");
Utils.warnUser("Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName());
Utils.warnUser("This calculation is critically dependent on being able to know when reference bases were inserted into SOLiD reads. Are you sure you want to proceed?");
warnUserNoColorSpace = true;
}
return originalQualScores;
}
/**
* Perform the SET_Q_ZERO solid recalibration. Inconsistent color space bases and their previous base are set to quality zero
* @param read The SAMRecord to recalibrate
@ -378,6 +379,7 @@ public class RecalDataManager {
readBases = BaseUtils.simpleReverseComplement( readBases.clone() ); // Put the bases back in reverse order to stuff them back in the read
}
read.setReadBases( readBases );
return originalQualScores;
}

3
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -107,6 +107,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
}
}
//TODO -- Add an integration test which tests SOLiD files that contain indels to make sure the Cigar string is processed correctly in the solid_recal_modes
// Currently we don't have any such data
@Test
public void testCountCovariatesVCF() {
HashMap<String, String> e = new HashMap<String, String>();