From b9544d3f89b8f433f750b2773610a3732ae4e16c Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 15 Oct 2009 16:47:29 +0000 Subject: [PATCH] Output formatting change (very slight) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1854 348d0f76-0448-11de-a6fe-93d51630548a --- .../PooledGenotypeConcordance.java | 40 +++++++++---------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java index 20444f65f..53c8ccecc 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/PooledGenotypeConcordance.java @@ -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");