zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #1101 from broadinstitute/ms_remove_KBest_unique 

Removes unique(int maxSize) from KBestHaplotypeFinder
This commit is contained in:
Geraldine Van der Auwera 2015-07-28 17:27:48 -04:00
parent 9d9827f176 4d4de27ba3
commit ac86b22662
1 changed files with 10 additions and 36 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

46
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java
View File

@ -90,7 +90,7 @@ public class KBestHaplotypeFinder extends AbstractList<KBestHaplotype> implement
/**
* The top finder.
*
* <p>If there is only a single source vertex, its finder is the top finder. However whent there
* <p>If there is only a single source vertex, its finder is the top finder. However when there
* is more than one possible source, we create a composite finder that alternates between individual source vertices
* for their best haplotypes.</p>
*/
@ -472,44 +472,18 @@ public class KBestHaplotypeFinder extends AbstractList<KBestHaplotype> implement
* The resulting list is sorted by the score with more likely haplotype search results first.
* </p>
*
* @param maxSize maximum number of unique results to return.
*
* @throws IllegalArgumentException if {@code maxSize} is negative.
*
* @return never {@code null}, perhaps an empty list.
*/
public List<KBestHaplotype> unique(final int maxSize) {
if (maxSize < 0) throw new IllegalArgumentException("maxSize cannot be negative");
final int requiredCapacity = Math.min(maxSize,size());
final Set<Haplotype> haplotypes = new HashSet<>(requiredCapacity);
int resultSize = 0;
final List<KBestHaplotype> result = new ArrayList<>(requiredCapacity);
for (final KBestHaplotype kbh : this) {
if (haplotypes.add(kbh.haplotype())) {
result.add(kbh);
if (resultSize == maxSize) break;
}
}
return result;
}
/**
* Returns a unique list of haplotypes solutions.
*
* <p>
* The result will not contain more than one haplotype with the same base sequence. The solution of the best
* score is returned.
* </p>
* <p>
* This makes sense when there are more than one possible path through the graph to create the same haplotype.
* </p>
* <p>
* The resulting list is sorted by the score with more likely haplotype search results first.
* </p>
*
* @return never {@code null}, perhaps an empty list.
*/
public List<KBestHaplotype> unique() {
return unique(size());
final int requiredCapacity = size();
final Set<Haplotype> haplotypes = new HashSet<>(requiredCapacity);
final List<KBestHaplotype> result = new ArrayList<>(requiredCapacity);
for (final KBestHaplotype kbh : this) {
if (haplotypes.add(kbh.haplotype())) {
result.add(kbh);
}
}
return result;
}
}