zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Bug fixes and cleanups for IndelStatistics

This commit is contained in:
Guillermo del Angel 2011-08-18 16:28:40 -04:00
parent 58560a6d50
commit 626cbf9411
1 changed files with 23 additions and 47 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

70
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java
View File

@ -57,13 +57,13 @@ public class IndelStatistics extends VariantEvaluator {
private static final int IND_HET = 0; private static final int IND_HET = 0;
private static final int IND_INS = 1; private static final int IND_INS = 1;
private static final int IND_DEL = 2; private static final int IND_DEL = 2;
private static final int IND_AT_CG_RATIO = 3; private static final int IND_COMPLEX = 3;
private static final int IND_HET_INS = 4; private static final int IND_HET_INS = 4;
private static final int IND_HOM_INS = 5; private static final int IND_HOM_INS = 5;
private static final int IND_HET_DEL = 6; private static final int IND_HET_DEL = 6;
private static final int IND_HOM_DEL = 7; private static final int IND_HOM_DEL = 7;
private static final int IND_HOM_REF = 8; private static final int IND_HOM_REF = 8;
private static final int IND_COMPLEX = 9; private static final int IND_MIXED = 9;
private static final int IND_LONG = 10; private static final int IND_LONG = 10;
private static final int IND_AT_EXP = 11; private static final int IND_AT_EXP = 11;
private static final int IND_CG_EXP = 12; private static final int IND_CG_EXP = 12;
@ -86,7 +86,7 @@ public class IndelStatistics extends VariantEvaluator {
COLUMN_KEYS[0] = "heterozygosity"; COLUMN_KEYS[0] = "heterozygosity";
COLUMN_KEYS[1] = "insertions"; COLUMN_KEYS[1] = "insertions";
COLUMN_KEYS[2] = "deletions"; COLUMN_KEYS[2] = "deletions";
COLUMN_KEYS[3] = "AT_CG_expansion_ratio"; COLUMN_KEYS[3] = "complex";
COLUMN_KEYS[4] = "het_insertions"; COLUMN_KEYS[4] = "het_insertions";
COLUMN_KEYS[5] = "homozygous_insertions"; COLUMN_KEYS[5] = "homozygous_insertions";
COLUMN_KEYS[6] = "het_deletions"; COLUMN_KEYS[6] = "het_deletions";
@ -117,16 +117,7 @@ public class IndelStatistics extends VariantEvaluator {
return new String[]{"all"}; return new String[]{"all"};
} }
public Object getCell(int x, int y) { public Object getCell(int x, int y) {
final Object[] rowKeys = getRowKeys(); return String.format("%d",indelSummary[y]);
if (y == IND_AT_CG_RATIO) {
int at = indelSummary[IND_AT_EXP];
int cg = indelSummary[IND_CG_EXP];
return String.format("%4.2f",((double)at) / (Math.max(cg, 1)));
}
else
return String.format("%d",indelSummary[y]);
} }
/** /**
@ -165,40 +156,40 @@ public class IndelStatistics extends VariantEvaluator {
eventLength = -vc.getReference().length(); eventLength = -vc.getReference().length();
isDeletion = true; isDeletion = true;
} }
else { else if (vc.isComplexIndel()) {
indelSummary[IND_COMPLEX]++; indelSummary[IND_COMPLEX]++;
} }
else if (vc.isMixed())
indelSummary[IND_MIXED]++;
if (IndelUtils.isATExpansion(vc,ref)) if (IndelUtils.isATExpansion(vc,ref))
indelSummary[IND_AT_EXP]++; indelSummary[IND_AT_EXP]++;
if (IndelUtils.isCGExpansion(vc,ref)) if (IndelUtils.isCGExpansion(vc,ref))
indelSummary[IND_CG_EXP]++; indelSummary[IND_CG_EXP]++;
// make sure event doesn't overstep array boundaries // make sure event doesn't overstep array boundaries
if (Math.abs(eventLength) < INDEL_SIZE_LIMIT) { if (vc.isSimpleDeletion() || vc.isSimpleInsertion()) {
indelSummary[len2Index(eventLength)]++; if (Math.abs(eventLength) < INDEL_SIZE_LIMIT) {
if (eventLength % 3 != 0) indelSummary[len2Index(eventLength)]++;
indelSummary[IND_FRAMESHIFT]++; if (eventLength % 3 != 0)
indelSummary[IND_FRAMESHIFT]++;
}
else
indelSummary[IND_LONG]++;
} }
else
indelSummary[IND_LONG]++;
} }
} }
static class IndelClasses implements TableType { static class IndelClasses implements TableType {
protected final static String ALL_SAMPLES_KEY = "allSamples";
protected final static String[] columnNames = IndelUtils.getIndelClassificationNames(); protected final static String[] columnNames = IndelUtils.getIndelClassificationNames();
// map of sample to statistics // map of sample to statistics
protected final HashMap<String, int[]> indelClassSummary = new HashMap<String, int[]>(); protected final int[] indelClassSummary;
public IndelClasses(final VariantContext vc) { public IndelClasses(final VariantContext vc) {
indelClassSummary.put(ALL_SAMPLES_KEY, new int[columnNames.length]); indelClassSummary = new int[columnNames.length];
for( final String sample : vc.getGenotypes().keySet() ) {
indelClassSummary.put(sample, new int[columnNames.length]);
}
} }
/** /**
@ -206,11 +197,10 @@ public class IndelStatistics extends VariantEvaluator {
* @return one row per sample * @return one row per sample
*/ */
public Object[] getRowKeys() { public Object[] getRowKeys() {
return indelClassSummary.keySet().toArray(new String[indelClassSummary.size()]); return new String[]{"all"};
} }
public Object getCell(int x, int y) { public Object getCell(int x, int y) {
final Object[] rowKeys = getRowKeys(); return String.format("%d",indelClassSummary[y]);
return String.format("%d",indelClassSummary.get(rowKeys[x])[y]);
} }
/** /**
@ -234,18 +224,7 @@ public class IndelStatistics extends VariantEvaluator {
} }
private void incrementSampleStat(VariantContext vc, int index) { private void incrementSampleStat(VariantContext vc, int index) {
indelClassSummary.get(ALL_SAMPLES_KEY)[index]++; indelClassSummary[index]++;
for( final String sample : vc.getGenotypes().keySet() ) {
if ( indelClassSummary.containsKey(sample) ) {
Genotype g = vc.getGenotype(sample);
boolean isVariant = (g.isCalled() && !g.isHomRef());
if (isVariant)
// update count
indelClassSummary.get(sample)[index]++;
}
}
} }
/* /*
* increment the specified value * increment the specified value
@ -293,16 +272,13 @@ public class IndelStatistics extends VariantEvaluator {
if (eval != null ) { if (eval != null ) {
if ( indelStats == null ) { if ( indelStats == null ) {
int nSamples = numSamples; indelStats = new IndelStats(eval);
if ( nSamples != -1 )
indelStats = new IndelStats(eval);
} }
if ( indelClasses == null ) { if ( indelClasses == null ) {
indelClasses = new IndelClasses(eval); indelClasses = new IndelClasses(eval);
} }
if ( eval.isIndel() && eval.isBiallelic() ) { if ( eval.isIndel() || eval.isMixed() ) {
if (indelStats != null ) if (indelStats != null )
indelStats.incrValue(eval, ref); indelStats.incrValue(eval, ref);