Output formatting changed:
- summary output now reported as a percentage rather than proportion; 2 sigfigs - fixed minor bug where FNR was calculated over total calls rather than total variant sites - column headers are_now_contiguous_strings - spacing fixed - "No Call" separated from "Ref Call" as its own column git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1644 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl
parent
73bec6f36d
commit
534486a254
|
|
@ -89,9 +89,9 @@ public class PooledGenotypeConcordance extends BasicVariantAnalysis implements G
|
|||
}
|
||||
|
||||
class PooledConcordanceTable {
|
||||
private final int CALL_INDECES = 5;
|
||||
private final int CALL_INDECES = 6;
|
||||
private final int TRUTH_INDECES = 4;
|
||||
private final int NO_CALL = 0;
|
||||
private final int NO_CALL = 5;
|
||||
private final int REF_CALL = 0; // synonym
|
||||
private final int VARIANT_CALL_NONHAPMAP = 1;
|
||||
private final int VARIANT_CALL_MATCH = 2;
|
||||
|
|
@ -299,35 +299,40 @@ class PooledConcordanceTable {
|
|||
nFullHapmapRefSites += table[TRUTH_REF][callIndex];
|
||||
}
|
||||
|
||||
int nRefsCalledCorrectly = table[TRUTH_REF][NO_CALL];
|
||||
int nRefsCalledCorrectly = table[TRUTH_REF][REF_CALL];
|
||||
int nHapmapRefsNotCalled = table[TRUTH_REF][NO_CALL];
|
||||
int nRefsCalledAsSNP = table[TRUTH_REF][VARIANT_CALL];
|
||||
int nSNPsCalledCorrectly = table[TRUTH_VAR][VARIANT_CALL_MATCH];
|
||||
int nSNPsCalledIncorrectly = table[TRUTH_VAR][VARIANT_CALL_MISMATCH];
|
||||
int nSNPsCalledAsRef = table[TRUTH_VAR][REF_CALL];
|
||||
int nHapmapSNPsNotCalled = table[TRUTH_VAR][NO_CALL];
|
||||
int nSNPsOnHapmapSNP = table[TRUTH_VAR][VARIANT_CALL_MATCH] + table[TRUTH_VAR][VARIANT_CALL_MISMATCH];
|
||||
int nSNPsAtNonHapmap = table[NO_TRUTH_DATA][VARIANT_CALL_NONHAPMAP];
|
||||
int nSNPsAtHapmapWithRefDataOnSubsetOfIndividuals = table[TRUTH_UNKNOWN][VARIANT_CALL_UNKNOWN];
|
||||
|
||||
out.add(String.format("| Total Number of SNP Calls: %d", nSNPCallSites));
|
||||
out.add(String.format("| Total SNP calls on non-Hapmap sites %d", nSNPsAtNonHapmap));
|
||||
out.add(String.format("| Number of Hapmap Sites: %d", nHapmapSites));
|
||||
out.add(String.format("| Total Number of SNP Calls:\t\t%d", nSNPCallSites));
|
||||
out.add(String.format("| Total SNP calls on non-Hapmap sites\t\t%d", nSNPsAtNonHapmap));
|
||||
out.add(String.format("| Number of Hapmap Sites:\t\t%d", nHapmapSites));
|
||||
out.add("| Data on Hapmap Reference Sites");
|
||||
out.add(String.format("| \t+ Sites where all Hapmap chips were ref: %d", nFullHapmapRefSites));
|
||||
out.add(String.format("| \t\t- Reference sites correctly called: %d (%f)", nRefsCalledCorrectly, ((double)nRefsCalledCorrectly/nFullHapmapRefSites)));
|
||||
out.add(String.format("| \t\t- Reference sites called as variant: %d (%f)", nRefsCalledAsSNP, ((double)nRefsCalledAsSNP/nFullHapmapRefSites)));
|
||||
out.add(String.format("| \t+ Sites where all Hapmap chips were ref: \t\t%d", nFullHapmapRefSites));
|
||||
out.add(String.format("| \t\t- Reference sites correctly called:\t\t%d\t(%d%%)", nRefsCalledCorrectly, divideToPercent(nRefsCalledCorrectly, nFullHapmapRefSites)));
|
||||
out.add(String.format("| \t\t- Reference sites called as variant:\t\t%d\t(%d%%)", nRefsCalledAsSNP, divideToPercent(nRefsCalledAsSNP, nFullHapmapRefSites)));
|
||||
out.add(String.format("| \t\t- Reference sites not confidently called:\t%d\t(%f)", nHapmapRefsNotCalled, ((double)nHapmapRefsNotCalled)/nFullHapmapRefSites));
|
||||
out.add(String.format("| \t+ Sites where all seen Hapmap chips were ref, but not all Hapmap chips available: %d", nUnknownHapmapSites));
|
||||
out.add(String.format("| \t\t- Putative reference sites called ref: %d (%f)", table[TRUTH_UNKNOWN][REF_CALL], ((double)table[TRUTH_UNKNOWN][REF_CALL]/nUnknownHapmapSites)));
|
||||
out.add(String.format("| \t\t- Putative reference sites called SNP: %d (%f)", nSNPsAtHapmapWithRefDataOnSubsetOfIndividuals, ((double)nSNPsAtHapmapWithRefDataOnSubsetOfIndividuals/nUnknownHapmapSites)));
|
||||
out.add(String.format("| \t\t- Putative reference sites called ref:\t\t\t%d\t(%d%%)", table[TRUTH_UNKNOWN][REF_CALL], divideToPercent(table[TRUTH_UNKNOWN][REF_CALL], nUnknownHapmapSites)));
|
||||
out.add(String.format("| \t\t- Putative reference sites called SNP:\t\t\t%d\t(%d%%)", nSNPsAtHapmapWithRefDataOnSubsetOfIndividuals, divideToPercent(nSNPsAtHapmapWithRefDataOnSubsetOfIndividuals, nUnknownHapmapSites)));
|
||||
out.add(String.format("| \t\t- Putative reference sites not confidently called:\t%d\t(%d%%)", table[TRUTH_UNKNOWN][NO_CALL], divideToPercent(table[TRUTH_UNKNOWN][NO_CALL], nUnknownHapmapSites)));
|
||||
out.add("| Data on Hapmap Variant Sites");
|
||||
out.add(String.format("| \t+ Number of Hapmap SNP Sites: %d", nHapmapSNPSites));
|
||||
out.add(String.format("| \t\t- SNP sites incorrectly called ref: %d (%f)", nSNPsCalledAsRef, ((double)nSNPsCalledAsRef/nHapmapSNPSites)));
|
||||
out.add(String.format("| \t+ SNP calls on Hapmap SNP Sites: %d", nSNPsOnHapmapSNP));
|
||||
out.add(String.format("| \t\t- SNP sites correctly called SNP: %d (%f)", nSNPsCalledCorrectly, ((double)nSNPsCalledCorrectly/nSNPsOnHapmapSNP)));
|
||||
out.add(String.format("| \t\t- SNP sites called a different base: %d (%f)", nSNPsCalledIncorrectly, ((double)nSNPsCalledIncorrectly/nSNPsOnHapmapSNP)));
|
||||
out.add(String.format("| Calls on reference N: %d", variantCallsAtRefN));
|
||||
out.add(String.format("| \t+ Number of Hapmap SNP Sites:\t\t\t%d", nHapmapSNPSites));
|
||||
out.add(String.format("| \t\t- SNP sites incorrectly called ref:\t%d\t(%d%%)", nSNPsCalledAsRef, divideToPercent(nSNPsCalledAsRef, nHapmapSNPSites)));
|
||||
out.add(String.format("| \t\t- SNP sites not confidently called:\t%d\t(%d%%)", nHapmapSNPsNotCalled, divideToPercent(nHapmapSNPsNotCalled, nHapmapSNPSites)));
|
||||
out.add(String.format("| \t+ SNP calls on Hapmap SNP Sites:\t\t%d", nSNPsOnHapmapSNP));
|
||||
out.add(String.format("| \t\t- SNP sites correctly called SNP:\t%d\t(%d%%)", nSNPsCalledCorrectly, divideToPercent(nSNPsCalledCorrectly, nSNPsOnHapmapSNP)));
|
||||
out.add(String.format("| \t\t- SNP sites called a different base:\t%d\t(%d%%)", nSNPsCalledIncorrectly, divideToPercent(nSNPsCalledIncorrectly, nSNPsOnHapmapSNP)));
|
||||
out.add(String.format("| Calls on reference N:\t\t%d", variantCallsAtRefN));
|
||||
out.add("----------------------- Output By Allele Frequency ------------------------");
|
||||
out.add("");
|
||||
out.add("FREQUENCY \tFALSE POSITIVES\tTRUE NEGATIVES\tFALSE NEGATIVES\tTRUE POSITIVES\tMISCALLS\tFALSE NEGATIVE RATE\tFALSE POSITIVE RATE");
|
||||
out.add("FREQUENCY \tFALSE_POSITIVES\tTRUE_NEGATIVES\tFALSE_NEGATIVES\tTRUE_POSITIVES\tMISCALLS\tNO_CALLS\tFALSE_NEGATIVE_RATE\tFALSE_POSITIVE_RATE");
|
||||
for( int i = 0; i < getLargestOutputAlleleFrequencyIndex(); i ++) {
|
||||
double freq = freqIndexToFrequency(i);
|
||||
int nRefsCalledAsSNPFreq = tableByHMFrequency[i][TRUTH_REF][VARIANT_CALL];
|
||||
|
|
@ -335,11 +340,17 @@ class PooledConcordanceTable {
|
|||
int nSNPsCalledIncorrectlyFreq = tableByHMFrequency[i][TRUTH_VAR][VARIANT_CALL_MISMATCH];
|
||||
int nSNPsCalledCorrectlyFreq = tableByHMFrequency[i][TRUTH_VAR][VARIANT_CALL_MATCH];
|
||||
int nSNPsCalledAsRefFreq = tableByHMFrequency[i][TRUTH_VAR][REF_CALL];
|
||||
int nNoCallsAtFreq = tableByHMFrequency[i][TRUTH_VAR][NO_CALL] + tableByHMFrequency[i][TRUTH_REF][NO_CALL];
|
||||
int nSnpsCalledAtFreq = nSNPsCalledIncorrectlyFreq + nSNPsCalledCorrectlyFreq + nSNPsCalledAsRefFreq;
|
||||
double fnrate = ((double) nSNPsCalledAsRefFreq / nSnpsCalledAtFreq);
|
||||
double fprate = ((double) nRefsCalledAsSNPFreq / (nRefsCalledAsSNPFreq + nRefsCalledCorrectFreq));
|
||||
out.add(String.format("%f\t%d\t\t%d\t\t%d\t\t\t%d\t%d\t\t%f\t\t\t%f",
|
||||
freq, nRefsCalledAsSNPFreq, nRefsCalledCorrectFreq, nSNPsCalledAsRefFreq, nSNPsCalledCorrectlyFreq, nSNPsCalledIncorrectlyFreq, fnrate, fprate));
|
||||
int nSNPsAtFreq = 0;
|
||||
for( int j = 0; j < CALL_INDECES; j ++ ) {
|
||||
nSNPsAtFreq += tableByHMFrequency[i][TRUTH_VAR][j];
|
||||
}
|
||||
int nSNPsNoCallFreq = tableByHMFrequency[i][TRUTH_VAR][NO_CALL];
|
||||
double fnrate = ((double) (nSNPsNoCallFreq + nSNPsCalledAsRefFreq) / (nSNPsAtFreq));
|
||||
double fprate = ((double) nRefsCalledAsSNPFreq / (nRefsCalledAsSNPFreq + nRefsCalledCorrectFreq + tableByHMFrequency[i][TRUTH_REF][NO_CALL]));
|
||||
out.add(String.format("%f\t%d\t\t%d\t\t%d\t\t\t%d\t%d\t\t%d\t\t%f\t\t\t%f",
|
||||
freq, nRefsCalledAsSNPFreq, nRefsCalledCorrectFreq, nSNPsCalledAsRefFreq, nSNPsCalledCorrectlyFreq, nSNPsCalledIncorrectlyFreq, nNoCallsAtFreq, fnrate, fprate));
|
||||
}
|
||||
|
||||
return out;
|
||||
|
|
@ -357,4 +368,8 @@ class PooledConcordanceTable {
|
|||
|
||||
return freqIndex;
|
||||
}
|
||||
|
||||
public int divideToPercent( int numerator, int denominator ) {
|
||||
return (int) Math.floor(100.0*((double) numerator)/ denominator );
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue