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Merge pull request #425 from broadinstitute/ami_moleculo_project_changes 

Ami moleculo project changes (add 'final's based on review)
This commit is contained in:
amilev 2013-11-18 14:33:49 -08:00
parent cc85e373d0 e6ef37de1d
commit b603e6674d
2 changed files with 91 additions and 25 deletions
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15
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
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@ -101,11 +101,24 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
@Argument(fullName = "coverage_threshold", shortName = "cov", doc = "The minimum allowable coverage to be considered covered", required = false)
private int coverageThreshold = 20;
@Argument(fullName = "minBaseQuality", shortName = "minBQ", doc = "The minimum allowable base quality score to be counted for coverage",required = false)
private int minBaseQuality = 0;
@Argument(fullName = "minMappingQuality", shortName = "minMQ", doc = "The minimum allowable mapping quality score to be counted for coverage",required = false)
private int minMappingQuality = 0;
@Override
// Look to see if the region has sufficient coverage
public ActivityProfileState isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
int depth = context.getBasePileup().getBaseFilteredPileup(coverageThreshold).depthOfCoverage();
int depth;
if(minBaseQuality == 0 && minMappingQuality == 0)
depth = context.getBasePileup().getBaseFilteredPileup(coverageThreshold).depthOfCoverage();
else
depth = context.getBasePileup().getBaseAndMappingFilteredPileup(minBaseQuality,minMappingQuality).depthOfCoverage();
// note the linear probability scale
return new ActivityProfileState(ref.getLocus(), Math.min(depth / coverageThreshold, 1));

101
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
View File

@ -38,7 +38,10 @@ import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
/**
* Outputs the read lengths of all the reads in a file.
@ -77,51 +80,101 @@ public class ReadLengthDistribution extends ReadWalker<Integer, Integer> {
@Output
public PrintStream out;
private GATKReport report;
//A map from RG to its column number (its index in an int[] array)
private Map<SAMReadGroupRecord,Integer> readGroupsLocation;
//Each line in the table is a read length and each column it the number of reads of a specific RG with that length. Thus a table is a map between read lengths to array of values (one for each RG).
private Map<Integer,int[]> table;
private List<SAMReadGroupRecord> readGroups;
public void initialize() {
final List<SAMReadGroupRecord> readGroups = getToolkit().getSAMFileHeader().getReadGroups();
readGroups = getToolkit().getSAMFileHeader().getReadGroups();
readGroupsLocation = new HashMap<>();
table = new TreeMap<>();
int readGroupsNum = 0;
report = new GATKReport();
report.addTable("ReadLengthDistribution", "Table of read length distributions", 1 + (readGroups.isEmpty() ? 1 : readGroups.size()));
GATKReportTable table = report.getTable("ReadLengthDistribution");
table.addColumn("readLength");
if (readGroups.isEmpty())
table.addColumn("SINGLE_SAMPLE");
else
for (SAMReadGroupRecord rg : readGroups)
table.addColumn(rg.getSample());
}
public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
return ( !read.getReadPairedFlag() || read.getReadPairedFlag() && read.getFirstOfPairFlag());
if (!readGroups.isEmpty()){
for (SAMReadGroupRecord rg : readGroups){
readGroupsLocation.put(rg,readGroupsNum);
readGroupsNum++;
}
}
}
@Override
public Integer map(ReferenceContext referenceContext, GATKSAMRecord samRecord, RefMetaDataTracker RefMetaDataTracker) {
GATKReportTable table = report.getTable("ReadLengthDistribution");
public Integer map(final ReferenceContext referenceContext,final GATKSAMRecord samRecord,final RefMetaDataTracker RefMetaDataTracker) {
int length = Math.abs(samRecord.getReadLength());
String sample = samRecord.getReadGroup().getSample();
final int length = Math.abs(samRecord.getReadLength());
final SAMReadGroupRecord rg = samRecord.getReadGroup();
table.increment(length, sample);
increment(table,length, rg);
return null;
}
final private void increment(final Map<Integer,int[]> table,final int length,final SAMReadGroupRecord rg){
if(readGroupsLocation.isEmpty()){
if(table.containsKey(length))
table.get(length)[0]++;
else{
final int[] newLength = {1};
table.put(length,newLength);
}
}
else{
final int rgLocation = readGroupsLocation.get(rg);
if(table.containsKey(length))
table.get(length)[rgLocation]++;
else{
table.put(length,new int[readGroupsLocation.size()]);
table.get(length)[rgLocation]++;
}
}
}
@Override
public Integer reduceInit() {
return null;
}
@Override
public Integer reduce(Integer integer, Integer integer1) {
public Integer reduce(final Integer integer,final Integer integer1) {
return null;
}
public void onTraversalDone(Integer sum) {
public void onTraversalDone(final Integer sum) {
final GATKReport report = createGATKReport();
report.print(out);
}
final private GATKReport createGATKReport(){
final GATKReport report = new GATKReport();
report.addTable("ReadLengthDistribution", "Table of read length distributions", 1 + (readGroupsLocation.isEmpty() ? 1 : readGroupsLocation.size()));
final GATKReportTable tableReport = report.getTable("ReadLengthDistribution");
tableReport.addColumn("readLength");
if (readGroupsLocation.isEmpty()){
tableReport.addColumn("SINGLE_SAMPLE");
int rowIndex = 0;
for (Integer length : table.keySet()){
tableReport.set(rowIndex,0,length);
tableReport.set(rowIndex,1,table.get(length)[0]);
rowIndex++;
}
}
else{
for (SAMReadGroupRecord rg : readGroups)
tableReport.addColumn(rg.getSample());
int rowIndex = 0;
for (Integer length : table.keySet()){
tableReport.set(rowIndex,0,length);
for (int i=0; i < readGroupsLocation.size(); i++)
tableReport.set(rowIndex,i+1,table.get(length)[i]);
rowIndex++;
}
}
return report;
}
}