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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3555 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
sjia 2010-06-14 21:31:01 +00:00
parent c1046653a2
commit 8defb30796
3 changed files with 4 additions and 10 deletions
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3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
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@ -48,13 +48,10 @@ public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Lo
public boolean DEBUG = false;
@Argument(fullName = "debugAlleles", shortName = "debugAlleles", doc = "Print likelihood scores for these alleles", required = false)
public String inputAlleles = "";
@Argument(fullName = "ethnicity", shortName = "ethnicity", doc = "Use allele frequencies for this ethnic group", required = false)
public String ethnicity = "CaucasianUSA";
@Argument(fullName = "filter", shortName = "filter", doc = "file containing reads to exclude", required = false)
public String filterFile = "";
@Argument(fullName = "maxAllowedMismatches", shortName = "maxAllowedMismatches", doc = "Max number of mismatches tolerated per read (default 7)", required = false)
public int MAXALLOWEDMISMATCHES = 6;
@Argument(fullName = "minRequiredMatches", shortName = "minRequiredMatches", doc = "Min number of matches required per read (default 7)", required = false)
public int MINREQUIREDMATCHES = 0;

3
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestHLAWalker.java
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@ -60,9 +60,6 @@ public class FindClosestHLAWalker extends ReadWalker<Integer, Integer> {
@Argument(fullName = "onlyfrequent", shortName = "onlyfrequent", doc = "Only consider alleles with frequency > 0.0001", required = false)
public boolean ONLYFREQUENT = false;
@Argument(fullName = "HLAfrequencies", shortName = "HLAfrequencies", doc = "HLA allele frequencies file", required = true)
public String AlleleFrequencyFile = "HLA_FREQUENCIES.txt";
@Argument(fullName = "HLAdictionary", shortName = "HLAdictionary", doc = "HLA dictionary file", required = true)
public String HLAdatabaseFile = "HLA_DICTIONARY.txt";

8
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java
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@ -57,8 +57,8 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
@Argument(fullName = "debugAlleles", shortName = "debugAlleles", doc = "Print likelihood scores for these alleles", required = false)
public String debugAlleles = "";
@Argument(fullName = "phaseInterval", shortName = "phaseInterval", doc = "Use only these intervals in phase calculation", required = false)
public String phaseIntervalFile = "";
@Argument(fullName = "useInterval", shortName = "useInterval", doc = "Use only these intervals in phase calculation", required = false)
public String IntervalsFile = "";
@Argument(fullName = "onlyfrequent", shortName = "onlyfrequent", doc = "Only consider alleles with frequency > 0.0001", required = false)
public boolean ONLYFREQUENT = false;
@ -174,9 +174,9 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
//Load genomic intervals for bam file
if (!phaseIntervalFile.equals("")){
if (!IntervalsFile.equals("")){
TextFileReader fileReader = new TextFileReader();
fileReader.ReadFile(phaseIntervalFile);
fileReader.ReadFile(IntervalsFile);
String[] lines = fileReader.GetLines();
intervals = new int[lines.length][2];
for (int i = 0; i < lines.length; i++) {