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Fix up Sherman's new docs in compliance with javadoc specs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2368 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-12-15 21:20:38 +00:00
parent df79ed8db1
commit cf46472419
7 changed files with 14 additions and 38 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/BaseLikelihoodsFileReader.java
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@ -1,13 +1,9 @@
/*
* Reads the .baselikelihoods file for various walkers in the HLA caller suite
*/
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import java.io.*;
import java.util.ArrayList;
/**
*
* Reads the .baselikelihoods file for various walkers in the HLA caller suite
* @author shermanjia
*/
public class BaseLikelihoodsFileReader {

9
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateAlleleLikelihoodsWalker.java
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@ -1,9 +1,5 @@
/*
* Calculates likelihood of observing the data given pairs of HLA alleles. NOTE: run CalculateBaseLikelihoods first! Usage: java -jar GenomeAnalysisTK.jar -T CalculateAlleleLikelihoods -I /humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.nuc.imputed.4digit.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl INPUT.baselikelihoods -eth\
nicity Caucasian | grep -v "INFO" | grep -v "DONE!" > OUTPUT.allelelikelihoods
*/
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
@ -13,7 +9,8 @@ import java.util.Hashtable;
/**
*
* Calculates likelihood of observing the data given pairs of HLA alleles. NOTE: run CalculateBaseLikelihoods first! Usage: java -jar GenomeAnalysisTK.jar -T CalculateAlleleLikelihoods -I /humgen/gsa-scr1/GSA/sjia/454_HLA/HLA/HLA.nuc.imputed.4digit.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl INPUT.baselikelihoods -eth\
nicity Caucasian | grep -v "INFO" | grep -v "DONE!" > OUTPUT.allelelikelihoods
* @author shermanjia
*/
@Requires({DataSource.READS, DataSource.REFERENCE})

7
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculateBaseLikelihoodsWalker.java
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@ -1,8 +1,5 @@
/*
* Calculates the probability of observing data for each genotype at every position. NOTE: run FindClosestAllele first to create .filter file. Usage: java -jar GenomeAnalysisTK.jar -T CalculateBaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval [-filter INPUT.filter -minAllowedMismatches 7] | grep -v "INFO" | grep -v "MISALIGNED" > OUTPUT.baselikelihoods
*/
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -18,7 +15,7 @@ import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
/**
*
* Calculates the probability of observing data for each genotype at every position. NOTE: run FindClosestAllele first to create .filter file. Usage: java -jar GenomeAnalysisTK.jar -T CalculateBaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval [-filter INPUT.filter -minAllowedMismatches 7] | grep -v "INFO" | grep -v "MISALIGNED" > OUTPUT.baselikelihoods
* @author shermanjia
*/
public class CalculateBaseLikelihoodsWalker extends LocusWalker<Integer, Pair<Long, Long>>{

9
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CalculatePhaseLikelihoodsWalker.java
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@ -1,9 +1,5 @@
/*
* Calculates the likelihood of observing data given phase info from pairs of HLA alleles. Note: Run FindClosestAlleleWalker first! Usage: java -jar $GATK -T CalculatePhaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -phaseInterval /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl IMPUT.baselikelihoods [-filter $ID.filter -minAllowe\
dMismatches 7] -ethnicity Caucasian | grep -v "INFO" | grep -v "DEBUG" | grep -v "DONE!" > OUTPUT.phaselikelihoods
*/
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.GATKArgumentCollection;
@ -13,7 +9,8 @@ import java.util.ArrayList;
import java.util.Hashtable;
/**
*
* Calculates the likelihood of observing data given phase info from pairs of HLA alleles. Note: Run FindClosestAlleleWalker first! Usage: java -jar $GATK -T CalculatePhaseLikelihoods -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -phaseInterval /humgen/gsa-scr1/GSA/sjia/454_HLA/HAPMAP270/HLA_exons.interval -bl IMPUT.baselikelihoods [-filter $ID.filter -minAllowe\
dMismatches 7] -ethnicity Caucasian | grep -v "INFO" | grep -v "DEBUG" | grep -v "DONE!" > OUTPUT.phaselikelihoods
* @author shermanjia
*/
@Requires({DataSource.READS, DataSource.REFERENCE})

9
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreatePedFileWalker.java
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@ -1,9 +1,5 @@
/**
* Creates a ped file of SNPs and amino acids coded as SNPs given an input ped file with 4-digit HLA alleles. Usage: java -jar GenomeAnalysisTK.jar -T CreatePedFile --allelesFile INPUT.ped -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-sc\
r1/GSA/sjia/454_HLA/HLA/HLA.combined.4digitUnique.bam > OUTPUT.log
*/
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
@ -12,7 +8,8 @@ import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Enumeration;
/**
*
* Creates a ped file of SNPs and amino acids coded as SNPs given an input ped file with 4-digit HLA alleles. Usage: java -jar GenomeAnalysisTK.jar -T CreatePedFile --allelesFile INPUT.ped -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-sc\
r1/GSA/sjia/454_HLA/HLA/HLA.combined.4digitUnique.bam > OUTPUT.log
* @author shermanjia
*/
@Requires({DataSource.READS, DataSource.REFERENCE})

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FindClosestAlleleWalker.java
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@ -1,7 +1,3 @@
/**
* Finds the most similar HLA allele for each read. Usage: java -jar GenomeAnalysisTK.jar -T FindClosestAllele -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L INPUT.interval -findFirst | grep -v INFO | sort -k1 > OUTPUT
*/
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import net.sf.samtools.SAMRecord;
@ -11,7 +7,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.util.ArrayList;
import java.util.Hashtable;
/**
*
* Finds the most similar HLA allele for each read. Usage: java -jar GenomeAnalysisTK.jar -T FindClosestAllele -I INPUT.bam -R /broad/1KG/reference/human_b36_both.fasta -L INPUT.interval -findFirst | grep -v INFO | sort -k1 > OUTPUT
* @author shermanjia
*/
@Requires({DataSource.READS, DataSource.REFERENCE})

6
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/FrequencyFileReader.java
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@ -1,13 +1,9 @@
/**
* File reader used by other Walkers to read HLA allele frequencies.
*/
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import java.io.*;
import java.util.Hashtable;
/**
*
* File reader used by other Walkers to read HLA allele frequencies.
* @author shermanjia
*/
public class FrequencyFileReader {