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Merged bug fix from Stable into Unstable

This commit is contained in:
Chris Hartl 2013-10-10 13:01:12 -04:00
parent e9a93d23c3 06d28c7f8b
commit 55bab9fa87
1 changed files with 10 additions and 3 deletions
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13
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
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@ -81,8 +81,9 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
* wherein unknown parents needn't be specified. The columns are the individual ID, and a list of key-value pairs.
* </p><p>
* Regardless of which file is specified, the walker will output a .fam file alongside the bed file. If the
* command line has "-md [name].fam", the fam file will simply be copied. However, if a metadata file of the
* alternate format is passed by "-md [name].txt", the walker will construct a formatted .fam file from the data.
* command line has "-md [name].fam", the fam file will be subset and reordered to match the sample content and ordering
* of the VCF. However, if a metadata file of the alternate format is passed by "-md [name].txt", the walker will
* construct a formatted .fam file from the data.
* </p>
*/
@Input(shortName="m",fullName = "metaData",required=true,doc="Sample metadata file. You may specify a .fam file " +
@ -170,6 +171,13 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
if ( ! sampleMetaValues.containsKey(sample) ) {
throw new UserException("No metadata provided for sample "+sample);
}
Map<String,String> mVals = sampleMetaValues.get(sample);
String fid = mVals.containsKey("fid") ? mVals.get("fid") : String.format("dummy_%d",++dummyID);
String pid = mVals.containsKey("dad") ? mVals.get("dad") : String.format("dummy_%d",++dummyID);
String mid = mVals.containsKey("mom") ? mVals.get("mom") : String.format("dummy_%d",++dummyID);
String sex = mVals.containsKey("sex") ? mVals.get("sex") : "3";
String pheno = mVals.containsKey("phenotype") ? mVals.get("phenotype") : "-1";
outFam.printf("%s\t%s\t%s\t%s\t%s\t%s%n",fid,sample,pid,mid,sex,pheno);
}
if ( mode == OutputMode.INDIVIDUAL_MAJOR ) {
// only need to instantiate the files and buffers if in individual major.
@ -469,7 +477,6 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
values.put("sex",sex);
values.put("phenotype",pheno);
metaValues.put(sid,values);
outFam.printf("%s%n",line);
}
} else {
for ( String line : new XReadLines(metaDataFile) ) {