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Removing unused class 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5197 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-02-04 22:22:28 +00:00
parent 0ad1ea4aa1
commit fe4aa58d35
3 changed files with 146 additions and 95 deletions
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94
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/SAMFileReader.java
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@ -1,94 +0,0 @@
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broadinstitute.sting.playground.gatk.walkers.HLAcaller;
import java.io.*;
import java.util.ArrayList;
/**
*
* @author shermanjia
*/
public class SAMFileReader {
ArrayList<String> ReadStrings = new ArrayList<String>();
ArrayList<String> CigarStrings = new ArrayList<String>();
ArrayList<String> ReadNames = new ArrayList<String>();
ArrayList<Integer> ReadStartPositions = new ArrayList<Integer>();
ArrayList<Integer> ReadStopPositions = new ArrayList<Integer>();
int minstartpos;
int maxstoppos;
CigarParser formatter = new CigarParser();
public String[] GetReads(){
return ReadStrings.toArray(new String[ReadStrings.size()]);
}
public String[] GetReadNames(){
return ReadNames.toArray(new String[ReadNames.size()]);
}
public String[] GetCigarStrings(){
return CigarStrings.toArray(new String[CigarStrings.size()]);
}
public Integer[] GetStartPositions(){
return ReadStartPositions.toArray(new Integer[ReadStartPositions.size()]);
}
public Integer[] GetStopPositions(){
return ReadStopPositions.toArray(new Integer[ReadStopPositions.size()]);
}
public Integer GetMinStartPos(){
return minstartpos;
}
public Integer GetMaxStopPos(){
return maxstoppos;
}
public int GetReadIndex(String readname){
if (ReadNames.contains(readname)){
return ReadNames.indexOf(readname);
}else{
return -1;
}
}
public void ReadFile(String filename){
try{
FileInputStream fstream = new FileInputStream(filename);
DataInputStream in = new DataInputStream(fstream);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
String strLine; String [] s = null;
//Read File Line By Line
int i = 0;
while ((strLine = br.readLine()) != null) {
s = strLine.split("\\t");
if (s.length>=10){
//Parse the reads with cigar parser
String read = formatter.FormatRead(s[5],s[9]);
ReadStrings.add(read);
CigarStrings.add(s[5]);
ReadNames.add(s[0]);
ReadStartPositions.add(Integer.valueOf(s[3]));
ReadStopPositions.add(Integer.valueOf(s[3]) + read.length() - 1);
if (i == 0){
minstartpos = Integer.valueOf(s[3]);
maxstoppos = Integer.valueOf(Integer.valueOf(s[3]) + read.length() - 1);
}
minstartpos = Math.min(minstartpos, Integer.valueOf(s[3]));
maxstoppos = Math.max(maxstoppos, Integer.valueOf(Integer.valueOf(s[3]) + read.length() - 1));
i++;
}
}
in.close();
}catch (Exception e){//Catch exception if any
System.err.println("SAMFileReader Error: " + e.getMessage());
}
}
}

145
scala/qscript/oneoffs/depristo/CleaningTest.scala 100755
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@ -0,0 +1,145 @@
package oneoffs.depristo
//import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import collection.JavaConversions._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.function.JarCommandLineFunction
class CleaningTest extends QScript {
qscript =>
@Input(doc="path to GATK jar", shortName="gatk", required=false)
var gatkJar: File = new File("/home/radon01/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/dist/GenomeAnalysisTK.jar")
@Input(doc="the chromosome to process", shortName="chr", required=false)
var chr: String = "20"
@Input(doc="the chromosome to process", shortName="L", required=false)
var range: String = _
@Input(doc="output path", shortName="outputDir", required=false)
var outputDir: String = "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/isizeConstrainedRealigner/"
@Input(doc="base output filename", shortName="baseName", required=false)
var baseName: String = ""
@Input(doc="path to tmp space for storing intermediate bam files", shortName="outputTmpDir", required=false)
var outputTmpDir: String = "/broad/shptmp/depristo/tmp"
@Input(doc="path to Picard FixMateInformation.jar. See http://picard.sourceforge.net/ .", required=false)
var picardFixMatesJar: File = new java.io.File("/seq/software/picard/current/bin/FixMateInformation.jar")
var picardValidateJar: File = new java.io.File("/seq/software/picard/current/bin/ValidateSamFile.jar")
var picardSortSamJar: File = new java.io.File("/seq/software/picard/current/bin/SortSam.jar")
private val tmpDir: File = new File("/broad/shptmp/depristo/tmp/")
private val reference: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
private val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
private val dindelEURCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110111_august_dindel_indel_calls/EUR.dindel_august_release.20110110.sites.vcf.gz"
// val chromosomeLength = List(249250621,243199373,198022430,191154276,180915260,171115067,159138663,146364022,141213431,135534747,135006516,133851895,115169878,107349540,102531392,90354753,81195210,78077248,59128983,63025520,48129895,51304566)
// private var pipeline: Pipeline = _
trait CommandLineGATKArgs extends CommandLineGATK {
this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.reference
this.memoryLimit = Some(4)
this.jobTempDir = qscript.tmpDir
}
def script = {
val interval = qscript.chr
val bamList: File = new File("/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/isizeConstrainedRealigner/CEU.chr%s.list".format(qscript.chr))
//val bamList: File = new File("/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/isizeConstrainedRealigner/FIN.chr%s.3samples.list".format(qscript.chr))
val targetIntervals: File = new File("%s/chr_%s.intervals".format(outputDir, qscript.chr))
Console.println("interval " + interval)
// 1.) Create cleaning targets
var target = new RealignerTargetCreator with CommandLineGATKArgs
target.input_file :+= bamList
target.intervalsString :+= interval
target.out = targetIntervals
target.mismatchFraction = Some(0.0)
target.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP)
target.rodBind :+= RodBind("indels3", "VCF", qscript.dindelEURCalls)
//target.jobName = baseName + ".target"
add(target)
for ( cm <- List(true, false) ) {
// 2.) Clean without SW
var clean = new IndelRealigner with CommandLineGATKArgs
val cleanedBam = new File(outputDir + "cleaned.cm_%b.bam".format(cm))
clean.input_file :+= bamList
clean.intervalsString :+= interval + (if ( range != null ) ":" + range else "")
clean.targetIntervals = targetIntervals
clean.out = if ( cm ) cleanedBam else new File(cleanedBam + ".intermediate.bam")
clean.doNotUseSW = true
clean.constrainMovement = cm
clean.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF)
clean.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP)
clean.rodBind :+= RodBind("indels3", "VCF", qscript.dindelEURCalls)
//clean.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true
//clean.jobName = baseName + cm + ".clean"
Console.println("CLEAN")
add(clean)
if ( ! cm ) {
// Explicitly run fix mates if the function won't be scattered.
val fixMates = new PicardBamJarFunction {
// Declare inputs/outputs for dependency tracking.
@Input(doc="unfixed bam") var unfixed: File = _
@Output(doc="fixed bam") var fixed: File = _
def inputBams = List(unfixed)
def outputBam = fixed
}
//fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
fixMates.memoryLimit = Some(4)
fixMates.jarFile = qscript.picardFixMatesJar
fixMates.unfixed = clean.out
fixMates.fixed = cleanedBam
//fixMates.analysisName = "FixMates"
// Add the fix mates explicitly
Console.println("fixMates")
add(fixMates)
}
val validate = new JarCommandLineFunction {
// Declare inputs/outputs for dependency tracking.
@Input(doc="unfixed bam") var unfixed: File = _
def inputBams = List(unfixed)
override def commandLine = super.commandLine + "%s%s%s IGNORE=INVALID_CIGAR IGNORE=MATE_NOT_FOUND".format(
optional(" VALIDATION_STRINGENCY=", "SILENT"), repeat(" INPUT=", inputBams), " TMP_DIR=" + jobTempDir)
}
//fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
validate.memoryLimit = Some(2)
validate.jarFile = qscript.picardValidateJar
validate.unfixed = cleanedBam
add(validate)
val toQueryName = new PicardBamJarFunction {
// Declare inputs/outputs for dependency tracking.
@Input(doc="coordiante bam") var cobam: File = _
@Output(doc="query bam") var qnbam: File = _
def inputBams = List(cobam)
def outputBam = qnbam
}
//fixMates.jobOutputFile = new File(".queue/logs/Cleaning/%s/FixMates.out".format(sampleId))
toQueryName.memoryLimit = Some(4)
toQueryName.jarFile = qscript.picardSortSamJar
toQueryName.cobam = cleanedBam
toQueryName.qnbam = new File(cleanedBam.getAbsolutePath + ".qn.bam")
add(toQueryName)
Console.println("loop done")
}
}
}

2
scala/qscript/oneoffs/depristo/VQSRCutByNRS.scala
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@ -5,7 +5,7 @@ import org.broadinstitute.sting.queue.QScript
import org.apache.commons.io.FilenameUtils;
import scala.io.Source._
class recalibrate extends QScript {
class VQSRCutByNRS extends QScript {
// @Input(doc="bamIn", shortName="I", required=true)
// var bamList: File = _