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

-Support for 1KG SNP calls in RODs 

-Minor bug fix


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@987 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-11 18:56:37 +00:00
parent 5440dd13df
commit ffffe3b2f6
3 changed files with 14 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
View File

@ -66,6 +66,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
addModule("RefSeq", rodRefSeq.class);
addModule("Table", TabularROD.class);
addModule("PooledEM", PooledEMSNPROD.class);
addModule("1KGSNPs", KGenomesSNPROD.class);
addModule("Intervals", IntervalRod.class);
}

16
java/src/org/broadinstitute/sting/gatk/refdata/TabularROD.java
View File

@ -41,7 +41,7 @@ import org.apache.log4j.Logger;
public class TabularROD extends BasicReferenceOrderedDatum implements Map<String, String> {
private static Logger logger = Logger.getLogger(TabularROD.class);
private GenomeLoc loc;
protected GenomeLoc loc;
private HashMap<String, String> attributes;
private ArrayList<String> header;
@ -176,7 +176,15 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
if ( header != null ) {
logger.debug(String.format("HEADER IS %s%n", Utils.join(":", header)));
} else {
throw new RuntimeException("Couldn't find header line in TabularROD!");
// use the indexes as the header fields
logger.debug("USING INDEXES FOR ROD HEADER");
// reset if necessary
if ( !reader.hasNext() )
reader = new xReadLines(source);
header = new ArrayList<String>();
int tokens = reader.next().split(DELIMITER_REGEX).length;
for ( int i = 0; i < tokens; i++)
header.add(Integer.toString(i));
}
return header;
@ -188,6 +196,7 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
//
// ----------------------------------------------------------------------
public GenomeLoc getLocation() {
loc = GenomeLoc.parseGenomeLoc(get(header.get(0)));
return loc;
}
@ -282,8 +291,7 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
throw new IOException(String.format("Header length %d not equal to Tabular parts length %d", header.size(), parts.length));
}
loc = GenomeLoc.parseGenomeLoc(parts[0]);
for ( int i = 1; i < parts.length; i++ ) {
for ( int i = 0; i < parts.length; i++ ) {
put(header.get(i), parts[i]);
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -111,7 +111,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
updateAnalysisSet(ALL_SNPS, eval, tracker, ref, context);
if ( eval instanceof SNPCallFromGenotypes ) {
SNPCallFromGenotypes call = (PooledEMSNPROD)eval;
SNPCallFromGenotypes call = (SNPCallFromGenotypes)eval;
int nVarGenotypes = call.nHetGenotypes() + call.nHomVarGenotypes();
//System.out.printf("%d variant genotypes at %s%n", nVarGenotypes, calls);
final String s = nVarGenotypes == 1 ? SINGLETON_SNPS : TWOHIT_SNPS;