diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java index d0b7e252f..f089dda56 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java @@ -500,15 +500,15 @@ public class CoverageStatistics extends LocusWalker, CoverageA int[] leftEnds = stats.getEndpoints(); StringBuilder hBuilder = new StringBuilder(); hBuilder.append("\t"); - hBuilder.append(String.format("[0,%d)\t",leftEnds[0])); + hBuilder.append(String.format("from_0_to_%d)\t",leftEnds[0])); for ( int i = 1; i < leftEnds.length; i++ ) - hBuilder.append(String.format("[%d,%d)\t",leftEnds[i-1],leftEnds[i])); - hBuilder.append(String.format("[%d,inf)%n",leftEnds[leftEnds.length-1])); + hBuilder.append(String.format("from_%d_to_%d)\t",leftEnds[i-1],leftEnds[i])); + hBuilder.append(String.format("from_%d_to_inf%n",leftEnds[leftEnds.length-1])); output.print(hBuilder.toString()); Map histograms = stats.getHistograms(); for ( String s : histograms.keySet() ) { StringBuilder sBuilder = new StringBuilder(); - sBuilder.append(String.format("%s",s)); + sBuilder.append(String.format("sample_%s",s)); for ( int count : histograms.get(s) ) { sBuilder.append(String.format("\t%d",count)); } @@ -532,9 +532,9 @@ public class CoverageStatistics extends LocusWalker, CoverageA // columns - depth of coverage StringBuilder header = new StringBuilder(); - header.append(String.format("\t>=0")); + header.append(String.format("\tgte_0")); for ( int d : endpoints ) { - header.append(String.format("\t>=%d",d)); + header.append(String.format("\tgte_%d",d)); } header.append(String.format("%n")); diff --git a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatisticsIntegrationTest.java b/java/test/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatisticsIntegrationTest.java index 24e68f2b8..8b67bb82b 100644 --- a/java/test/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatisticsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatisticsIntegrationTest.java @@ -60,13 +60,13 @@ public class CoverageStatisticsIntegrationTest extends WalkerTest { spec.addAuxFile("959937a9b0ace520b4b7d9915d708003", baseOutputFile); spec.addAuxFile("aff2349d6dc221c08f6c469379aeaedf", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics")); spec.addAuxFile("6476ed0c54a4307a618aa6d3268b050f", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary")); - spec.addAuxFile("c744a298b7541f3f823e6937e9a0bc67", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_locus_statistics")); + spec.addAuxFile("50870dad272f03f77befb0075baed1cd", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_locus_statistics")); spec.addAuxFile("65318c1e73d98a59cc6f817cde12d3d4", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary_statistics")); - spec.addAuxFile("9fc19f773a7ddfbb473d124e675a3d94", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); + spec.addAuxFile("ef8c3e2ba3fc0da829e10e2d487c00d2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics")); spec.addAuxFile("223377e07b35e81a394b75b38d8e72ee", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_statistics")); spec.addAuxFile("096f4ed94020327288ea76245ebd6942", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_interval_summary")); - spec.addAuxFile("437b92f70a6c414de9178a12c02511c2", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_locus_statistics")); - spec.addAuxFile("cf1d038e278f28f382f79c30d8416b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); + spec.addAuxFile("06ed004c86f8b2ad8e64a3b42a0d85c5", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_locus_statistics")); + spec.addAuxFile("43c160ff9d754744728c142709011993", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_statistics")); spec.addAuxFile("a374410efe20609c5c4b87a6da7f4d51", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".read_group_summary")); execute("testBaseOutputNoFiltering",spec);