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

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
View File

@ -57,7 +57,7 @@ public class RecalDataManager {
private static boolean warnUserNullReadGroup = false; private static boolean warnUserNullReadGroup = false;
private static boolean warnUserNoColorSpace = 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() { RecalDataManager() {
data = new NestedHashMap(); data = new NestedHashMap();
@ -251,6 +251,7 @@ public class RecalDataManager {
* @param read The SAMRecord to parse * @param read The SAMRecord to parse
*/ */
public static void parseColorSpace( final SAMRecord read ) { 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 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.getReadGroup().getPlatform().equalsIgnoreCase("SOLID") ) {
if( read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null ) { // Haven't calculated the inconsistency array yet for this read 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 ); read.setAttribute( RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency );
} else if ( !warnUserNoColorSpace ) { // Warn the user if we can't find the color space tag } 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("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("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; warnUserNoColorSpace = true;
} }
} }
@ -337,14 +338,14 @@ public class RecalDataManager {
} }
} else if ( !warnUserNoColorSpace ) { // Warn the user if we can't find the color space tag } 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("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("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; warnUserNoColorSpace = true;
} }
return originalQualScores; return originalQualScores;
} }
/** /**
* Perform the SET_Q_ZERO solid recalibration. Inconsistent color space bases and their previous base are set to quality zero * 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 * @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 readBases = BaseUtils.simpleReverseComplement( readBases.clone() ); // Put the bases back in reverse order to stuff them back in the read
} }
read.setReadBases( readBases ); read.setReadBases( readBases );
return originalQualScores; 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 @Test
public void testCountCovariatesVCF() { public void testCountCovariatesVCF() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();