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Transposing the table, and fixing some null pointer exceptions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4906 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-12-23 16:22:57 +00:00
parent cebfd01857
commit 6ebf5b30de
1 changed files with 45 additions and 28 deletions
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73
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/ACTransitionTable.java
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@ -34,11 +34,11 @@ public class ACTransitionTable extends VariantEvaluator {
@DataPoint(name="Het transitions",description="AC[s] = AC[s-1]+1 and AC[s] = AC[s-1]+2 transitions") @DataPoint(name="Het transitions",description="AC[s] = AC[s-1]+1 and AC[s] = AC[s-1]+2 transitions")
TransitionTable transitions = null; TransitionTable transitions = null;
@DataPoint(name="Private permutations",description="Marginal increase in number of sites per sample") @DataPoint(name="Private permutations",description="Marginal increase in number of sites per sample")
PermutationCounts privatePermutations = new PermutationCounts(1,transitions); PermutationCounts privatePermutations;
@DataPoint(name="AC2 Permutations",description="Marginal increase in number of AC=2 sites, per sample") @DataPoint(name="AC2 Permutations",description="Marginal increase in number of AC=2 sites, per sample")
PermutationCounts doubletonPermutations = new PermutationCounts(2,transitions); PermutationCounts doubletonPermutations;
@DataPoint(name="AC3 Permutations",description="Marginal increase in number of tripleton sites, per sample") @DataPoint(name="AC3 Permutations",description="Marginal increase in number of tripleton sites, per sample")
PermutationCounts tripletonPermutations = new PermutationCounts(3,transitions); PermutationCounts tripletonPermutations;
String[][] permutations; String[][] permutations;
@ -73,13 +73,16 @@ public class ACTransitionTable extends VariantEvaluator {
for ( String sample : ordering ) { for ( String sample : ordering ) {
if ( eval.getGenotype(sample).isHet() ) { if ( eval.getGenotype(sample).isHet() ) {
variant_ac++; variant_ac++;
transitions.hetTransitionCounts[order_offset][sample_offset][variant_ac-1]++; transitions.hetTransitionCounts[order_offset][variant_ac-1][sample_offset]++;
} else if ( eval.getGenotype(sample).isHomVar() ) { } else if ( eval.getGenotype(sample).isHomVar() ) {
variant_ac += 2; variant_ac += 2;
transitions.homTransitionCounts[order_offset][sample_offset][variant_ac-1]++; transitions.homTransitionCounts[order_offset][variant_ac-1][sample_offset]++;
} else { } else {
// todo -- note, unclear how to treat no calls. Is the hom in het,ref,ref,nocall,hom sample 4 or 5? // todo -- note, unclear how to treat no calls. Is the hom in het,ref,ref,nocall,hom sample 4 or 5?
transitions.stationaryCounts[order_offset][sample_offset][variant_ac-1]++; // todo -- do we want to tabulate P[sample i is not variant | some variant]? This is just combinatorics so i left it out
if ( variant_ac > 0 ) {
transitions.stationaryCounts[order_offset][variant_ac-1][sample_offset]++;
}
} }
sample_offset ++; sample_offset ++;
} }
@ -133,13 +136,16 @@ public class ACTransitionTable extends VariantEvaluator {
} }
transitions = new TransitionTable(); transitions = new TransitionTable();
transitions.hetTransitionCounts = new int[NUM_PERMUTATIONS][permuteSamples.size()][2*permuteSamples.size()]; transitions.hetTransitionCounts = new int[NUM_PERMUTATIONS][permuteSamples.size()*2][permuteSamples.size()];
transitions.homTransitionCounts = new int[NUM_PERMUTATIONS][permuteSamples.size()][2*permuteSamples.size()]; transitions.homTransitionCounts = new int[NUM_PERMUTATIONS][permuteSamples.size()*2][permuteSamples.size()];
transitions.stationaryCounts = new int[NUM_PERMUTATIONS][permuteSamples.size()][2*permuteSamples.size()]; transitions.stationaryCounts = new int[NUM_PERMUTATIONS][permuteSamples.size()*2][permuteSamples.size()];
privatePermutations = new PermutationCounts(1,transitions);
doubletonPermutations = new PermutationCounts(2,transitions);
tripletonPermutations = new PermutationCounts(3,transitions);
} }
public void finalizeEvaluation() { public void finalizeEvaluation() { // note: data points are null when this is called (wtf?)
veWalker.getLogger().info(String.format("Skipped: %d",skipped)); veWalker.getLogger().info(String.format("Skipped: %d",skipped));
} }
class TransitionTable implements TableType { class TransitionTable implements TableType {
@ -154,13 +160,13 @@ public class ACTransitionTable extends VariantEvaluator {
if ( rowKeys == null ) { if ( rowKeys == null ) {
rowKeys = new String[3*hetTransitionCounts[0].length]; rowKeys = new String[3*hetTransitionCounts[0].length];
for ( int i = 0; i < hetTransitionCounts[0].length; i ++ ) { for ( int i = 0; i < hetTransitionCounts[0].length; i ++ ) {
rowKeys[i] = String.format("%s%d%s","Sample_",i,"_(het)"); rowKeys[i] = String.format("%s%d%s","AC_",i,"_(het)");
} }
for ( int i = 0; i < hetTransitionCounts[0].length; i ++ ) { for ( int i = 0; i < hetTransitionCounts[0].length; i ++ ) {
rowKeys[i] = String.format("%s%d%s","Sample_",i,"_(hom)"); rowKeys[hetTransitionCounts[0].length+i] = String.format("%s%d%s","AC_",i,"_(hom)");
} }
for ( int i = 0; i < hetTransitionCounts[0].length; i ++ ) { for ( int i = 0; i < hetTransitionCounts[0].length; i ++ ) {
rowKeys[i] = String.format("%s%d%s","Sample_",i,"_(ref)"); rowKeys[2*hetTransitionCounts[0].length+i] = String.format("%s%d%s","AC_",i,"_(ref)");
} }
} }
@ -170,27 +176,31 @@ public class ACTransitionTable extends VariantEvaluator {
public String getCell(int x, int y) { public String getCell(int x, int y) {
if ( countAverages == null ) { if ( countAverages == null ) {
countAverages = new String[hetTransitionCounts[0].length][hetTransitionCounts[0][0].length]; countAverages = new String[hetTransitionCounts[0].length*3][hetTransitionCounts[0][0].length];
for ( int idx = 0; idx < hetTransitionCounts[0][0].length; idx ++) { for ( int sam = 0; sam < hetTransitionCounts[0][0].length; sam ++) {
for ( int sam = 0 ; sam < hetTransitionCounts[0].length; sam ++ ) { for ( int idx = 0 ; idx < hetTransitionCounts[0].length; idx ++ ) {
int totalTimesAtACSample = 0; int totalTimesAtACSample = 0;
int totalStationary = 0; int totalStationary = 0;
int totalAC1Shift = 0; int totalAC1Shift = 0;
int totalAC2Shift = 0; int totalAC2Shift = 0;
for ( int p = 0; p < hetTransitionCounts.length; p++ ) { for ( int p = 0; p < hetTransitionCounts.length; p++ ) {
totalStationary += stationaryCounts[p][sam][idx]; totalStationary += stationaryCounts[p][idx][sam];
totalAC2Shift += (idx+2 > hetTransitionCounts[0][0].length) ? 0 : homTransitionCounts[p][sam][idx+2]; totalAC2Shift += (idx+2 >= hetTransitionCounts[0][0].length) ? 0 : homTransitionCounts[p][idx+2][sam];
totalAC1Shift += (idx+1 > hetTransitionCounts[0][0].length) ? 0 : hetTransitionCounts[p][sam][idx+1]; totalAC1Shift += (idx+1 >= hetTransitionCounts[0][0].length) ? 0 : hetTransitionCounts[p][idx+1][sam];
} }
totalTimesAtACSample = totalStationary+totalAC1Shift+totalAC2Shift; totalTimesAtACSample = totalStationary+totalAC1Shift+totalAC2Shift;
countAverages[sam][idx] = String.format("%.4f", ((double) totalAC1Shift)/totalTimesAtACSample); countAverages[idx][sam] = formatProp(totalAC1Shift,totalTimesAtACSample);
countAverages[sam][hetTransitionCounts[0][0].length+idx] = String.format("%.4f", ((double) totalAC2Shift)/totalTimesAtACSample); countAverages[hetTransitionCounts[0].length+idx][sam] = formatProp(totalAC2Shift,totalTimesAtACSample);
countAverages[sam][hetTransitionCounts[0][0].length*2+idx] = String.format("%.4f",((double)totalStationary)/totalTimesAtACSample); countAverages[hetTransitionCounts[0].length*2+idx][sam] = formatProp(totalStationary,totalTimesAtACSample);
} }
} }
} }
return countAverages[x][y]; return countAverages[x][y] == null ? "0.00" : countAverages[x][y];
}
private String formatProp(int num, int denom) {
return (denom != 0) ? String.format("%.4f", ((double) num)/denom) : "0.0";
} }
public String getName() { return "AC Transition Tables"; } public String getName() { return "AC Transition Tables"; }
@ -199,7 +209,7 @@ public class ACTransitionTable extends VariantEvaluator {
if ( colKeys == null ) { if ( colKeys == null ) {
colKeys = new String[hetTransitionCounts[0][0].length]; colKeys = new String[hetTransitionCounts[0][0].length];
for ( int ac = 0; ac < hetTransitionCounts[0][0].length; ac ++ ) { for ( int ac = 0; ac < hetTransitionCounts[0][0].length; ac ++ ) {
colKeys[ac] = String.format("AC%d",ac); colKeys[ac] = String.format("Sample_%d",ac);
} }
} }
@ -220,6 +230,7 @@ public class ACTransitionTable extends VariantEvaluator {
} }
public String[] getRowKeys() { public String[] getRowKeys() {
//System.out.printf("%s%n",table);
if ( rowNames == null ) { if ( rowNames == null ) {
rowNames = new String[table.stationaryCounts.length]; rowNames = new String[table.stationaryCounts.length];
for ( int p = 0 ; p < rowNames.length; p ++ ) { for ( int p = 0 ; p < rowNames.length; p ++ ) {
@ -232,7 +243,7 @@ public class ACTransitionTable extends VariantEvaluator {
public String[] getColumnKeys() { public String[] getColumnKeys() {
if ( colNames == null ) { if ( colNames == null ) {
colNames = new String[table.stationaryCounts[0].length]; colNames = new String[table.stationaryCounts[0][0].length];
for ( int s = 0 ; s < colNames.length; s ++ ) { for ( int s = 0 ; s < colNames.length; s ++ ) {
colNames[s] = String.format("Sample%d",s+1); colNames[s] = String.format("Sample%d",s+1);
} }
@ -242,13 +253,19 @@ public class ACTransitionTable extends VariantEvaluator {
} }
public Integer getCell(int x, int y) { public Integer getCell(int x, int y) {
return table.hetTransitionCounts[x][y][acToExtract-1] + return table.hetTransitionCounts[x][acToExtract-1][y] +
( (acToExtract > table.homTransitionCounts[0][0].length) ? 0 : table.homTransitionCounts[x][y][acToExtract-1]); ( (acToExtract > table.homTransitionCounts[0][0].length) ? 0 : table.homTransitionCounts[x][acToExtract-1][y]);
} }
public String getName() { public String getName() {
return String.format("PermutationCountsAC%d",acToExtract); return String.format("PermutationCountsAC%d",acToExtract);
} }
public void init() {
getRowKeys();
getColumnKeys();
getCell(1,1);
}
} }