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Debugging information is now written in such a way to make it easier to import into R. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@372 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-12 19:45:33 +00:00
parent 6ee4fe5a20
commit 35fc002d5d
2 changed files with 14 additions and 6 deletions
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18
java/src/org/broadinstitute/sting/playground/fourbasecaller/BasecallingBaseModel.java
View File

@ -167,22 +167,30 @@ public class BasecallingBaseModel {
PrintWriter writer = new PrintWriter(outparam); PrintWriter writer = new PrintWriter(outparam);
for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) { for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) {
writer.print("mean_" + baseIndexToBase(baseCurIndex) + " : [ "); writer.print("mean_" + baseIndexToBase(baseCurIndex) + " = c(");
for (int channel = 0; channel < 4; channel++) { for (int channel = 0; channel < 4; channel++) {
writer.print(sums[baseCurIndex].getQuick(channel)/counts[baseCurIndex]); writer.print(sums[baseCurIndex].getQuick(channel)/counts[baseCurIndex]);
writer.print(" ");
if (channel < 3) {
writer.print(", ");
}
} }
writer.print("] (" + counts[baseCurIndex] + ")\n"); writer.println(");");
DoubleMatrix2D cov = unscaledCovarianceSums[baseCurIndex].copy(); DoubleMatrix2D cov = unscaledCovarianceSums[baseCurIndex].copy();
cov.assign(F.div(counts[baseCurIndex])); cov.assign(F.div(counts[baseCurIndex]));
writer.println("cov_" + baseIndexToBase(baseCurIndex) + " : " + cov + "\n"); writer.print("cov_" + baseIndexToBase(baseCurIndex) + " = matrix(c(");
for (int channel1 = 0; channel1 < 4; channel1++) {
for (int channel2 = 0; channel2 < 4; channel2++) {
writer.print(cov.get(channel2, channel1) + (channel1 == 3 && channel2 == 3 ? "" : ","));
}
}
writer.println("), nr=4, nc=4);\n");
} }
writer.close(); writer.close();
} catch (IOException e) { } catch (IOException e) {
} }
} }

2
java/src/org/broadinstitute/sting/playground/fourbasecaller/BasecallingReadModel.java
View File

@ -81,7 +81,7 @@ public class BasecallingReadModel {
*/ */
public void write(File dir) { public void write(File dir) {
for (int cycle = 0; cycle < basemodels.length; cycle++) { for (int cycle = 0; cycle < basemodels.length; cycle++) {
File outparam = new File(dir.getPath() + "/param." + cycle); File outparam = new File(dir.getPath() + "/param." + cycle + ".r");
basemodels[cycle].write(outparam); basemodels[cycle].write(outparam);
} }
} }