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We can actually make this a bit simpler (and faster) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1943 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-30 04:21:03 +00:00
parent 1b6333e4ab
commit ccd7440730
1 changed files with 4 additions and 14 deletions
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18
java/src/org/broadinstitute/sting/playground/gatk/walkers/concordance/NWayVenn.java
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@ -22,13 +22,12 @@ import java.util.Map.Entry;
public class NWayVenn implements ConcordanceType { public class NWayVenn implements ConcordanceType {
// TODO -- change this to use Ryan's generic map object when it's ready // TODO -- change this to use Ryan's generic map object when it's ready
private HashMap<Integer, PrintWriter> writers = new HashMap<Integer, PrintWriter>(); private HashMap<String, PrintWriter> writers = new HashMap<String, PrintWriter>();
private PrintWriter union_writer = null;
private String prefix; private String prefix;
private int N; private int N;
private PrintWriter union_writer = null;
public NWayVenn() {} public NWayVenn() {}
public void initialize(String prefix, HashMap<String,String> args) { public void initialize(String prefix, HashMap<String,String> args) {
@ -59,7 +58,7 @@ public class NWayVenn implements ConcordanceType {
try { try {
for ( Entry<String, String> file : files.entrySet() ) for ( Entry<String, String> file : files.entrySet() )
writers.put(stringToHash(file.getKey()), new PrintWriter(prefix + "." + N + "wayVenn" + file.getValue() + ".calls")); writers.put(file.getKey(), new PrintWriter(prefix + "." + N + "wayVenn" + file.getValue() + ".calls"));
union_writer = new PrintWriter(prefix + "." + N + "wayVenn.union.calls"); union_writer = new PrintWriter(prefix + "." + N + "wayVenn.union.calls");
} catch (FileNotFoundException e) { } catch (FileNotFoundException e) {
throw new StingException(String.format("Could not open file(s) for writing")); throw new StingException(String.format("Could not open file(s) for writing"));
@ -87,7 +86,7 @@ public class NWayVenn implements ConcordanceType {
StringBuilder hashString = new StringBuilder(); StringBuilder hashString = new StringBuilder();
for (int i = 0; i < N; i++) for (int i = 0; i < N; i++)
hashString.append(calls[i] != null ? "1" : "0"); hashString.append(calls[i] != null ? "1" : "0");
printVariant(writers.get(stringToHash(hashString.toString())), calls); printVariant(writers.get(hashString.toString()), calls);
} }
private static void printVariant(PrintWriter writer, Variation[] variants) { private static void printVariant(PrintWriter writer, Variation[] variants) {
@ -104,13 +103,4 @@ public class NWayVenn implements ConcordanceType {
for ( PrintWriter writer : writers.values() ) for ( PrintWriter writer : writers.values() )
writer.close(); writer.close();
} }
private int stringToHash(String s) {
int hash = 0;
for (int i = 0; i < s.length(); i++) {
if ( s.charAt(i) == '1' )
hash += Math.pow(2, i);
}
return hash;
}
} }