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Fix for overflow issues 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2702 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-01-27 13:37:16 +00:00
parent 8453676b71
commit 40c242d2b8
1 changed files with 37 additions and 33 deletions
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70
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -46,6 +46,9 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
@Argument(fullName="suppressLocusPrinting", shortName= "noLocus", doc="Suppress printing", required=false) @Argument(fullName="suppressLocusPrinting", shortName= "noLocus", doc="Suppress printing", required=false)
public boolean suppressLocusPrinting = false; public boolean suppressLocusPrinting = false;
@Argument(fullName="suppressIntervalPrinting", shortName= "noInterval", doc="Suppress printing", required=false)
public boolean suppressIntervalPrinting = false;
@Argument(fullName="printBaseCounts", shortName ="bases", doc="Print individual base counts (A,C,G,T only)", required=false) @Argument(fullName="printBaseCounts", shortName ="bases", doc="Print individual base counts (A,C,G,T only)", required=false)
protected boolean printBaseCounts = false; protected boolean printBaseCounts = false;
@ -73,9 +76,9 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
private TreeSet<String> sampleNames = new TreeSet<String>(); private TreeSet<String> sampleNames = new TreeSet<String>();
// keep track of the histogram data // keep track of the histogram data
private ExpandingArrayList<Integer> coverageHist = null; private ExpandingArrayList<Long> coverageHist = null;
private int maxDepth = 0; private long maxDepth = 0;
private int totalLoci = 0; private long totalLoci = 0;
// we want to see reads with deletions // we want to see reads with deletions
public boolean includeReadsWithDeletionAtLoci() { return true; } public boolean includeReadsWithDeletionAtLoci() { return true; }
@ -84,7 +87,7 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
// initialize histogram array // initialize histogram array
if ( printHistogram ) { if ( printHistogram ) {
coverageHist = new ExpandingArrayList<Integer>(); coverageHist = new ExpandingArrayList<Long>();
} }
// initialize read group names from BAM header // initialize read group names from BAM header
@ -120,7 +123,7 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
DoCInfo info = new DoCInfo(); DoCInfo info = new DoCInfo();
info.totalCoverage = pileup.size(); info.totalCoverage = pileup.size();
int nBadMAPQReads = 0, nDeletionReads = 0; long nBadMAPQReads = 0, nDeletionReads = 0;
for ( PileupElement p : pileup ) { for ( PileupElement p : pileup ) {
if ( excludeMAPQBelowThis > 0 && p.getRead().getMappingQuality() < excludeMAPQBelowThis ) if ( excludeMAPQBelowThis > 0 && p.getRead().getMappingQuality() < excludeMAPQBelowThis )
@ -140,14 +143,14 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
if ( byReadGroup ) { if ( byReadGroup ) {
String readGroupName = readGroup.getReadGroupId(); String readGroupName = readGroup.getReadGroupId();
int oldDepth = info.depthByReadGroup.get(readGroupName); long oldDepth = info.depthByReadGroup.get(readGroupName);
info.depthByReadGroup.put(readGroupName, oldDepth + 1); info.depthByReadGroup.put(readGroupName, oldDepth + 1);
} }
if ( bySample ) { if ( bySample ) {
String sample = readGroup.getSample(); String sample = readGroup.getSample();
if ( sample != null ) { if ( sample != null ) {
int oldDepth = info.depthBySample.get(sample); long oldDepth = info.depthBySample.get(sample);
info.depthBySample.put(sample, oldDepth + 1); info.depthBySample.put(sample, oldDepth + 1);
} }
} }
@ -189,13 +192,13 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
} }
if ( byReadGroup ) { if ( byReadGroup ) {
for ( String rg : readGroupNames ) { for ( String rg : readGroupNames ) {
int oldDepth = sum.depthByReadGroup.get(rg); long oldDepth = sum.depthByReadGroup.get(rg);
sum.depthByReadGroup.put(rg, oldDepth + value.depthByReadGroup.get(rg)); sum.depthByReadGroup.put(rg, oldDepth + value.depthByReadGroup.get(rg));
} }
} }
if ( bySample ) { if ( bySample ) {
for ( String sample : sampleNames ) { for ( String sample : sampleNames ) {
int oldDepth = sum.depthBySample.get(sample); long oldDepth = sum.depthBySample.get(sample);
sum.depthBySample.put(sample, oldDepth + value.depthBySample.get(sample)); sum.depthBySample.put(sample, oldDepth + value.depthBySample.get(sample));
} }
} }
@ -207,12 +210,14 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
public void onTraversalDone(List<Pair<GenomeLoc, DoCInfo>> results) { public void onTraversalDone(List<Pair<GenomeLoc, DoCInfo>> results) {
// build and print the per-interval header // build and print the per-interval header
out.println("\n\nPER_INTERVAL_COVERAGE_SECTION"); if ( ! suppressIntervalPrinting ) {
printHeaderLine(true); out.println("\n\nPER_INTERVAL_COVERAGE_SECTION");
printHeaderLine(true);
// print all of the individual per-interval coverage data // print all of the individual per-interval coverage data
for ( Pair<GenomeLoc, DoCInfo> result : results ) for ( Pair<GenomeLoc, DoCInfo> result : results )
printDoCInfo(result.first, result.second, true); printDoCInfo(result.first, result.second, true);
}
// if we need to print the histogram, do so now // if we need to print the histogram, do so now
if ( printHistogram ) if ( printHistogram )
@ -220,7 +225,6 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
} }
private void printHeaderLine(boolean printAverageCoverage) { private void printHeaderLine(boolean printAverageCoverage) {
StringBuilder header = new StringBuilder("location\ttotal_coverage"); StringBuilder header = new StringBuilder("location\ttotal_coverage");
if ( printAverageCoverage ) if ( printAverageCoverage )
header.append("\taverage_coverage"); header.append("\taverage_coverage");
@ -257,16 +261,16 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
out.println(header.toString()); out.println(header.toString());
} }
private void incCov(int depth) { private void incCov(long depth) {
int c = coverageHist.expandingGet(depth, 0); long c = coverageHist.expandingGet((int)depth, 0L);
coverageHist.set(depth, c + 1); coverageHist.set((int)depth, c + 1);
if ( depth > maxDepth ) if ( depth > maxDepth )
maxDepth = depth; maxDepth = depth;
totalLoci++; totalLoci++;
} }
private int getCov(int depth) { private long getCov(long depth) {
return coverageHist.get(depth); return coverageHist.get((int)depth);
} }
private void printHisto() { private void printHisto() {
@ -292,7 +296,7 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
long dist = (long)Math.pow(10, 9); long dist = (long)Math.pow(10, 9);
while ( Math.abs(getCov(mode) - getCov(1)) < dist && mode < maxDepth ) while ( Math.abs(getCov(mode) - getCov(1)) < dist && mode < maxDepth )
dist = Math.abs(getCov(mode++) - getCov(1)); dist = Math.abs(getCov(mode++) - getCov(1));
int maxGoodDepth = Math.min(mode + 1, maxDepth); long maxGoodDepth = Math.min(mode + 1, maxDepth);
// calculate the mean of the good region // calculate the mean of the good region
long totalGoodSites = 0, totalGoodDepth = 0; long totalGoodSites = 0, totalGoodDepth = 0;
@ -380,29 +384,29 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
} }
public class DoCInfo { public class DoCInfo {
public int totalCoverage = 0; public long totalCoverage = 0;
public int numDeletions = 0; public long numDeletions = 0;
public int numBadMQReads = 0; public long numBadMQReads = 0;
public int minDepthCoveredLoci = 0; public long minDepthCoveredLoci = 0;
public int[] baseCounts = null; public long[] baseCounts = null;
public HashMap<String, Integer> depthByReadGroup = null; public HashMap<String, Long> depthByReadGroup = null;
public HashMap<String, Integer> depthBySample = null; public HashMap<String, Long> depthBySample = null;
public DoCInfo() { public DoCInfo() {
if ( printBaseCounts ) { if ( printBaseCounts ) {
baseCounts = new int[4]; baseCounts = new long[4];
} }
if ( byReadGroup ) { if ( byReadGroup ) {
depthByReadGroup = new HashMap<String, Integer>(); depthByReadGroup = new HashMap<String, Long>();
for ( String readGroupName : readGroupNames ) for ( String readGroupName : readGroupNames )
depthByReadGroup.put(readGroupName, 0); depthByReadGroup.put(readGroupName, 0L);
} }
if ( bySample ) { if ( bySample ) {
depthBySample = new HashMap<String, Integer>(); depthBySample = new HashMap<String, Long>();
for ( String sample : sampleNames ) for ( String sample : sampleNames )
depthBySample.put(sample, 0); depthBySample.put(sample, 0L);
} }
} }