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Tweaks to formatting of output table. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1995 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-11-09 04:33:36 +00:00
parent 7ce0df76f8
commit 00a7113d7a
1 changed files with 8 additions and 9 deletions
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17
java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java
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@ -34,9 +34,6 @@ import cern.jet.stat.Probability;
* @author Kiran Garimella * @author Kiran Garimella
*/ */
public class FindContaminatingReadGroupsWalker extends LocusWalker<Integer, Integer> { public class FindContaminatingReadGroupsWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName="verbose", shortName="V", doc="Prints information for all loci, not just the suspected contaminating read groups", required=false)
private Boolean VERBOSE = false;
@Argument(fullName="balance", shortName="bal", doc="The expected alternate allele balance for homozygous-variant sites", required=false) @Argument(fullName="balance", shortName="bal", doc="The expected alternate allele balance for homozygous-variant sites", required=false)
private Double BALANCE = 0.95; private Double BALANCE = 0.95;
@ -157,7 +154,8 @@ public class FindContaminatingReadGroupsWalker extends LocusWalker<Integer, Inte
* @param result the number of suspicious sites we're inspecting (this argument is ignored) * @param result the number of suspicious sites we're inspecting (this argument is ignored)
*/ */
public void onTraversalDone(Integer result) { public void onTraversalDone(Integer result) {
if (VERBOSE) { out.println("#readgroup\tpvalue\tbalances"); } //out.println("readgroup\tpvalue\tstatus\tbalances");
out.printf("%-10s\t%-10s\t%-10s\t%-10s%n", "readgroup", "pvalue", "status", "balances");
for (String rg : altTable.getRowNames()) { for (String rg : altTable.getRowNames()) {
String balances = ""; String balances = "";
@ -199,11 +197,12 @@ public class FindContaminatingReadGroupsWalker extends LocusWalker<Integer, Inte
// Compute pValue // Compute pValue
double pValue = Probability.studentT(dof, t); double pValue = Probability.studentT(dof, t);
if (pValue < LIMIT) { //out.printf("%s\t%e\t%s\t[%s]\n", rg, pValue, (pValue < LIMIT ? "aberrant" : "nominal"), balances);
out.printf("%s\t%e\t[%s]\n", rg, pValue, balances); out.printf("%-10s\t%-10s\t%-10s\t[%-10s]\n",
} else { rg,
if (VERBOSE) { out.printf("#%s\t%e\t[%s]\n", rg, pValue, balances); } String.format("%e", pValue),
} (pValue < LIMIT ? "aberrant" : "nominal"),
balances);
} }
} }
} }