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Beautify the genotype concordance printouts 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1291 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-07-22 02:53:02 +00:00
parent 6e4fd8db4a
commit c54fd1da09
1 changed files with 44 additions and 17 deletions
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61
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -25,22 +25,26 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
private static final int TRUTH_VAR_HET = 1;
private static final int TRUTH_VAR_HOM = 2;
private static final int TRUTH_UNKNOWN = 3;
private static final String[] TRUTH_NAMES = {"IS_REF", "IS_VAR_HET", "IS_VAR_HOM", "UNKNOWN"};
private static final int CALL_REF = 0;
private static final int CALL_VAR_HET = 1;
private static final int CALL_VAR_HOM = 2;
private static final int CALL_NO_CONF = 3;
private static final int UNCALLABLE = 4;
private static final int NO_CALL = 3;
private static final String[] CALL_NAMES = {"CALLED_REF", "CALLED_VAR_HET", "CALLED_VAR_HOM", "NO_CALL"};
private int[][] table = new int[4][5];
private int[][] table = new int[4][4];
private int[] truth_totals = new int[4];
private int[] calls_totals = new int[4];
public GenotypeConcordance(final String name) {
super("genotype_concordance");
dbName = name;
for ( int i = 0; i < 4; i++ ) {
for ( int j = 0; j < 5; j++ ) {
truth_totals[i] = 0;
calls_totals[i] = 0;
for ( int j = 0; j < 4; j++ )
table[i][j] = 0;
}
}
}
@ -60,7 +64,7 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
// todo -- FIXME on countOccurences
if ( eval == null )
callIndex = UNCALLABLE;
callIndex = NO_CALL;
else if ( eval.isReference() && Utils.countOccurrences(ref, eval.getGenotype().get(0)) == eval.getGenotype().get(0).length() )
callIndex = CALL_REF;
else if ( isHet(eval) )
@ -69,9 +73,10 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
callIndex = CALL_VAR_HOM;
if ( chip != null || eval != null ) {
System.out.printf("TESTING ME: %d/%d %s vs. %s%n", truthIndex, callIndex, chip, eval);
//System.out.printf("TEST: %d/%d %s vs. %s%n", truthIndex, callIndex, chip, eval);
table[truthIndex][callIndex]++;
truth_totals[truthIndex]++;
calls_totals[callIndex]++;
}
}
@ -84,14 +89,39 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
public List<String> done() {
List<String> s = new ArrayList<String>();
s.add(String.format("name %s", dbName));
s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CONF\tUNCALLABLE"));
s.add(String.format("IS_REF\t\t%d\t\t%d\t\t%d\t\t%d\t\t%d", table[TRUTH_REF][CALL_REF], table[TRUTH_REF][CALL_VAR_HET], table[TRUTH_REF][CALL_VAR_HOM], table[TRUTH_REF][CALL_NO_CONF], table[TRUTH_REF][UNCALLABLE]));
s.add(String.format("IS_VAR_HET\t\t%d\t\t%d\t\t%d\t\t%d\t\t%d", table[TRUTH_VAR_HET][CALL_REF], table[TRUTH_VAR_HET][CALL_VAR_HET], table[TRUTH_VAR_HET][CALL_VAR_HOM], table[TRUTH_VAR_HET][CALL_NO_CONF], table[TRUTH_VAR_HET][UNCALLABLE]));
s.add(String.format("IS_VAR_HOM\t\t%d\t\t%d\t\t%d\t\t%d\t\t%d", table[TRUTH_VAR_HOM][CALL_REF], table[TRUTH_VAR_HOM][CALL_VAR_HET], table[TRUTH_VAR_HOM][CALL_VAR_HOM], table[TRUTH_VAR_HOM][CALL_NO_CONF], table[TRUTH_VAR_HOM][UNCALLABLE]));
s.add(String.format("UNKNOWN\t\t%d\t\t%d\t\t%d\t\t%d\t\t%d", table[TRUTH_UNKNOWN][CALL_REF], table[TRUTH_UNKNOWN][CALL_VAR_HET], table[TRUTH_UNKNOWN][CALL_VAR_HOM], table[TRUTH_UNKNOWN][CALL_NO_CONF], table[TRUTH_UNKNOWN][UNCALLABLE]));
s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL\t\t\tTOTALS"));
for (int i=0; i < 4; i++) {
StringBuffer sb = new StringBuffer();
sb.append(TRUTH_NAMES[i] + "\t");
for (int j=0; j < 4; j++)
sb.append(cellToString(table[i][j], truth_totals[i]) + "\t\t");
sb.append(truth_totals[i]);
s.add(sb.toString());
}
s.add("\n");
s.add(String.format("\t\tCALLED_REF\tCALLED_VAR_HET\tCALLED_VAR_HOM\tNO_CALL"));
for (int i=0; i < 4; i++) {
StringBuffer sb = new StringBuffer();
sb.append(TRUTH_NAMES[i] + "\t");
for (int j=0; j < 4; j++)
sb.append(cellToString(table[i][j], truth_totals[i]) + "\t\t");
s.add(sb.toString());
}
s.add(String.format("TOTALS\t%d\t\t%d\t\t%d\t\t%d", calls_totals[CALL_REF], calls_totals[CALL_VAR_HET], calls_totals[CALL_VAR_HOM], calls_totals[NO_CALL]));
return s;
}
private static String cellToString(int count, int total) {
StringBuffer sb = new StringBuffer();
sb.append(count + " (");
if ( total == 0 )
sb.append(0);
else
sb.append(100*count/total);
sb.append("%)");
return sb.toString();
}
private static boolean isHet(AllelicVariant var) {
if ( var instanceof Genotype )
return ((Genotype)var).isHet();
@ -100,9 +130,6 @@ public class GenotypeConcordance extends BasicVariantAnalysis implements Genotyp
if ( genotype.size() < 1 )
return false;
boolean het = genotype.get(0).charAt(0) != genotype.get(0).charAt(1);
System.out.printf("********* Genotype %s is het = %b%n", genotype, het);
return het;
return genotype.get(0).charAt(0) != genotype.get(0).charAt(1);
}
}