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Row/Column names are now R-friendly 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2966 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-03-09 19:01:03 +00:00
parent 0e360ea8af
commit 0a49dffa8f
2 changed files with 10 additions and 10 deletions
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12
java/src/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatistics.java
View File

@ -500,15 +500,15 @@ public class CoverageStatistics extends LocusWalker<Map<String,int[]>, 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<String,int[]> 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<Map<String,int[]>, 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"));

8
java/test/org/broadinstitute/sting/oneoffprojects/walkers/coverage/CoverageStatisticsIntegrationTest.java
View File

@ -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);