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

Use read group as a condition for confusion tables. With an integration test. 

Changed BaseTransitionTable to comparable objects for consistent ordering of output
( e.g. so the integration test doesn't yell so much )




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1889 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-20 19:39:32 +00:00
parent b83df5616a
commit 4a8a6468be
2 changed files with 47 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

41
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
View File

@ -42,6 +42,8 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
boolean usePileupMismatches = false;
@Argument(fullName="usePreviousReadBases", doc="Use previous bases of the read as part of the calculation. Will ignore reads if there aren't this many previous bases. Uses the specified number. Defaults to 0", required=false)
int nPreviousReadBases = 0;
@Argument(fullName="useReadGroup", doc="Use the group number of the read as a condition of the table.", required = false)
boolean useReadGroup = false;
private UnifiedGenotyper ug;
private ReferenceContextWindow refWindow;
@ -51,7 +53,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
ug = new UnifiedGenotyper();
ug.initialize();
refWindow = new ReferenceContextWindow(nPreviousBases);
conditionalTables = new HashSet<BaseTransitionTable>();
conditionalTables = new TreeSet<BaseTransitionTable>();
}
public Integer reduceInit() {
@ -146,7 +148,9 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
return false;
} else if ( read.getBaseQualities()[offset] <= minQualityScore ) {
return false;
} else {
} else if ( useSecondaryBase && read.getAttribute("SQ") == null )
return false;
else {
return true;
}
}
@ -173,6 +177,10 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
conditions.add(countMismatches(map.getPileup()));
}
if ( useReadGroup ) {
conditions.add(read.getReadGroup().getReadGroupId());
}
return conditions;
}
@ -195,6 +203,10 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
header = header + "\tNumber_of_pileup_mismatches";
}
if ( useReadGroup ) {
header = header + "\tRead_group";
}
return String.format("%s\t%s%n",header,"Counts");
}
@ -250,7 +262,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
}
class BaseTransitionTable {
class BaseTransitionTable implements Comparable {
private int[][] table;
private List<Comparable> conditions;
@ -286,6 +298,29 @@ class BaseTransitionTable {
}
}
public int compareTo(Object obj) {
if ( ! ( obj instanceof BaseTransitionTable ) ) {
return -1;
} else {
BaseTransitionTable t = (BaseTransitionTable) obj;
if ( this.conditionsMatch(t.conditions) ) {
return 0;
} else {
if ( this.numConditions() == t.numConditions() ) {
ListIterator<Comparable> thisIter = this.conditions.listIterator();
ListIterator<Comparable> thatIter = t.conditions.listIterator();
while ( thisIter.next() == thatIter.next() ) {
// do nothing
}
return thisIter.previous().compareTo(thatIter.previous());
} else {
return (this.numConditions() > t.numConditions() ) ? 1 : -1;
}
}
}
}
public void print( PrintStream out ) {
for ( char observedBase : BaseUtils.BASES ) {

10
java/test/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaIntegrationTest.java
View File

@ -21,6 +21,7 @@ public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest
public static final String OUTPUT_MD5_LOWCONFIDENTREFTHRESHOLD = "521a9fa7716ed22550c2ba3fe3409070";
public static final String OUTPUT_MD5_HIGHCONFIDENTREFTHRESHOLD = "8ab6d389fc494881736e9a58126c2f1b";
public static final String OUTPUT_MD5_ALLARGUMENTS = "f45481946d7a5c70078d432b0baff083";
public static final String OUTPUT_MD5_USEREADGROUP = "6dbf18e96f3367c8764b4d1e15eb956b";
public static final String LOCUS = "1:10,000,000-10,200,000";
public static final String BAM_FILE = "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam";
public static final String REFERENCE = "/broad/1KG/reference/human_b36_both.fasta";
@ -64,7 +65,7 @@ public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest
public void testBaseTransitionCalculatorJavaHighConfidentRefThreshold() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+ " --confidentRefThreshold 8";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_HIGHCONFIDENTREFTHRESHOLD));
executeTest("BaseTransitionTableCalculatorJava: Low Ref Threshold",spec);
executeTest("BaseTransitionTableCalculatorJava: High Ref Threshold",spec);
}
@Test
@ -73,4 +74,11 @@ public class BaseTransitionTableCalculatorJavaIntegrationTest extends WalkerTest
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_ALLARGUMENTS));
executeTest("BaseTransitionTableCalculatorJava: Low Ref Threshold, Low Q Score, Low Mapping Quality, Additional Mismatches",spec);
}
@Test
public void testBaseTransitionTableCalculatorJavaUseReadGroup() {
String args = "-T BaseTransitionTableCalculatorJava -o %s -I "+BAM_FILE+" -L "+LOCUS+" -R "+REFERENCE+" --useReadGroup";
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(args,1,Arrays.asList(OUTPUT_MD5_USEREADGROUP));
executeTest("testBaseTransitionTableCalculatorJava: Use read group", spec);
}
}