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Simplification of code segments; slight alteration to per-locus tabulation; added to-do items for cosmetic changes (mostly binning options and settigns) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2882 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-02-24 05:20:18 +00:00
parent 27d3ef9458
commit 5df37968de
1 changed files with 18 additions and 13 deletions
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31
java/src/org/broadinstitute/sting/oneoffprojects/walkers/CoverageStatistics.java
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@ -27,6 +27,7 @@ import java.util.Set;
* distribution of % bases and % targets covered for certain depths. The granularity of DOC can be set by command * distribution of % bases and % targets covered for certain depths. The granularity of DOC can be set by command
* line arguments. * line arguments.
* *
* // todo -- alter logarithmic scaling to spread out bins more
* // todo -- allow for user to set linear binning (default is logarithmic) * // todo -- allow for user to set linear binning (default is logarithmic)
* // todo -- add per target (e.g. regional) aggregation * // todo -- add per target (e.g. regional) aggregation
* *
@ -150,15 +151,16 @@ public class CoverageStatistics extends LocusWalker<Map<String,Integer>, DepthOf
// columns - depth of coverage // columns - depth of coverage
StringBuilder header = new StringBuilder(); StringBuilder header = new StringBuilder();
header.append(String.format("\t>=0"));
for ( int d : endpoints ) { for ( int d : endpoints ) {
header.append(String.format("\t%d",d)); header.append(String.format("\t>=%d",d));
} }
header.append(String.format("%n")); header.append(String.format("%n"));
output.print(header); output.print(header);
for ( int row = samples; row > 0; row ++ ) { for ( int row = 0; row < samples; row ++ ) {
output.printf("%s_%d\t","NSamples",row); output.printf("%s_%d\t","NSamples",row+1);
for ( int depthBin = 0; depthBin < baseCoverageCumDist[0].length; depthBin ++ ) { for ( int depthBin = 0; depthBin < baseCoverageCumDist[0].length; depthBin ++ ) {
output.printf("%d\t",baseCoverageCumDist[row][depthBin]); output.printf("%d\t",baseCoverageCumDist[row][depthBin]);
} }
@ -215,6 +217,8 @@ public class CoverageStatistics extends LocusWalker<Map<String,Integer>, DepthOf
bin++; bin++;
} }
bin = bin == histogram.length-1 ? histogram.length-2 : bin;
return bin; return bin;
} }
} }
@ -250,7 +254,8 @@ class DepthOfCoverageStats {
for ( int b = 1; b < bins ; b++ ) { for ( int b = 1; b < bins ; b++ ) {
int leftEnd = lower + (int) Math.floor(Math.pow(10.0,(b-1.0)*scale)); int leftEnd = lower + (int) Math.floor(Math.pow(10.0,(b-1.0)*scale));
// todo -- simplify to length^(scale/bins); make non-constant to put bin ends in more "useful"
// todo -- positions on the number line
while ( leftEnd <= binLeftEndpoints[b-1] ) { while ( leftEnd <= binLeftEndpoints[b-1] ) {
leftEnd++; leftEnd++;
} }
@ -281,7 +286,7 @@ class DepthOfCoverageStats {
return; return;
} }
int[] binCounts = new int[this.binLeftEndpoints.length]; int[] binCounts = new int[this.binLeftEndpoints.length+1];
for ( int b = 0; b < binCounts.length; b ++ ) { for ( int b = 0; b < binCounts.length; b ++ ) {
binCounts[b] = 0; binCounts[b] = 0;
} }
@ -291,9 +296,9 @@ class DepthOfCoverageStats {
} }
public void initializeLocusCounts() { public void initializeLocusCounts() {
locusCoverageCounts = new int[granularHistogramBySample.size()][binLeftEndpoints.length]; locusCoverageCounts = new int[granularHistogramBySample.size()][binLeftEndpoints.length+1];
locusHistogram = new int[binLeftEndpoints.length]; locusHistogram = new int[binLeftEndpoints.length+1];
for ( int b = 0; b < binLeftEndpoints.length; b ++ ) { for ( int b = 0; b < binLeftEndpoints.length+1; b ++ ) {
for ( int a = 0; a < granularHistogramBySample.size(); a ++ ) { for ( int a = 0; a < granularHistogramBySample.size(); a ++ ) {
locusCoverageCounts[a][b] = 0; locusCoverageCounts[a][b] = 0;
} }
@ -339,15 +344,15 @@ class DepthOfCoverageStats {
meanCoverages.put(sample,newMean); meanCoverages.put(sample,newMean);
int[] granularBins = granularHistogramBySample.get(sample); int[] granularBins = granularHistogramBySample.get(sample);
for ( int b = 1; b < granularBins.length; b ++ ) { for ( int b = 0; b < binLeftEndpoints.length; b ++ ) {
if ( depth < binLeftEndpoints[b] ) { if ( depth < binLeftEndpoints[b] ) {
granularBins[b-1]++; granularBins[b]++;
return b ; return b;
} }
} }
granularBins[granularBins.length-1]++; // greater than all left-endpoints granularBins[binLeftEndpoints.length]++; // greater than all left-endpoints
return granularBins.length-1; return binLeftEndpoints.length;
} }
public void merge(DepthOfCoverageStats newStats) { public void merge(DepthOfCoverageStats newStats) {