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

Output formatting change (very slight) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1854 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-15 16:47:29 +00:00
parent 839c5d66bc
commit b9544d3f89
1 changed files with 20 additions and 20 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

40
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java
View File

@ -326,26 +326,26 @@ class PooledConcordanceTable {
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:\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: \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 SNP:\t%d\t(%d%%)", nHapmapRefsNotCalled, divideToPercent(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:\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 SNP:\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:\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(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("\tSites where all Hapmap chips were ref: \t\t%d", nFullHapmapRefSites));
out.add(String.format("\t\tReference sites correctly called:\t\t%d\t(%d%%)", nRefsCalledCorrectly, divideToPercent(nRefsCalledCorrectly, nFullHapmapRefSites)));
out.add(String.format("\t\tReference sites called as variant:\t\t%d\t(%d%%)", nRefsCalledAsSNP, divideToPercent(nRefsCalledAsSNP, nFullHapmapRefSites)));
out.add(String.format("\t\tReference sites not confidently called SNP:\t%d\t(%d%%)", nHapmapRefsNotCalled, divideToPercent(nHapmapRefsNotCalled, nFullHapmapRefSites)));
out.add(String.format("\tSites where all seen Hapmap chips were ref, but not all Hapmap chips available: %d", nUnknownHapmapSites));
out.add(String.format("\t\tPutative 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\tPutative reference sites called SNP:\t\t\t%d\t(%d%%)", nSNPsAtHapmapWithRefDataOnSubsetOfIndividuals, divideToPercent(nSNPsAtHapmapWithRefDataOnSubsetOfIndividuals, nUnknownHapmapSites)));
out.add(String.format("\t\tPutative reference sites not confidently called SNP:\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("\tNumber of Hapmap SNP Sites:\t\t\t%d", nHapmapSNPSites));
out.add(String.format("\t\tSNP sites incorrectly called ref:\t%d\t(%d%%)", nSNPsCalledAsRef, divideToPercent(nSNPsCalledAsRef, nHapmapSNPSites)));
out.add(String.format("\t\tSNP sites not confidently called:\t%d\t(%d%%)", nHapmapSNPsNotCalled, divideToPercent(nHapmapSNPsNotCalled, nHapmapSNPSites)));
out.add(String.format("\tSNP calls on Hapmap SNP Sites:\t\t%d", nSNPsOnHapmapSNP));
out.add(String.format("\t\tSNP sites correctly called SNP:\t%d\t(%d%%)", nSNPsCalledCorrectly, divideToPercent(nSNPsCalledCorrectly, nSNPsOnHapmapSNP)));
out.add(String.format("\t\tSNP 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\tNO_CALLS\tFALSE_NEGATIVE_RATE\tFALSE_POSITIVE_RATE");