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very minor cleanup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4590 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-28 02:11:33 +00:00
parent cbce3e3c83
commit fe3cfb067c
2 changed files with 1 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
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@ -71,7 +71,7 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> implements Tre
@Argument(fullName="select", shortName="s", doc="Optionally specifies which subset of columns from which -B inputs should be used for annotations. For example, -B:mydbsnp,AnnotatorInputTable /path/to/mydbsnp.txt -B:mytable,AnnotatorInputTable /path/mytable.txt -s mydbsnp.avHet,mydbsnp.name,mytable.column3 will cause annotations to only be generated from the 3 columns specified using -s.", required=false)
protected String[] SELECT_COLUMNS = {};
@Argument(fullName="join", shortName="J", doc="Optionally specifies a file and column within that file that should be LEFT-JOIN'ed to a column in a previously-specified file. The file provided to -J must be tab-delimited, with the first non-comment/non-empty line containing column names. (example: -B name,AnnotatorInputTable,/path/to/file1 -J name2,/path/to/file2,name.columnName=name2.columnName2 - this will join the table in file2 to the table in file1) ", required=false)
@Argument(fullName="join", shortName="J", doc="Optionally specifies a file and column within that file that should be LEFT-JOIN'ed to a column in a previously-specified file. The file provided to -J must be tab-delimited, with the first non-comment/non-empty line containing column names. (example: -B:name,AnnotatorInputTable /path/to/file1 -J name2,/path/to/file2,name.columnName=name2.columnName2 - this will join the table in file2 to the table in file1) ", required=false)
protected String[] JOIN_ARGS = {};
@Argument(fullName="oneToMany", shortName="m", doc="If more than one record from the same file matches a particular locus (for example, multiple dbSNP records with the same position), create multiple entries in the ouptut VCF file - one for each match. If a particular tabular file has J matches, and another tabular file has K matches for a given locus, then J*K output VCF records will be generated - one for each pair of K, J. If this flag is not provided, the multiple records are still generated, but they are stored in the INFO field of a single output VCF record, with their annotation keys differentiated by appending '_i' with i varying from 1 to K*J. ", required=false)

1
java/src/org/broadinstitute/sting/utils/MathUtils.java
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@ -31,7 +31,6 @@ import java.math.BigDecimal;
import java.util.*;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.playground.gatk.walkers.genotyper.AlleleFrequencyCalculationModel;
/**
* MathUtils is a static class (no instantiation allowed!) with some useful math methods.