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Cleanup. Remove some unnecessary methods. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2900 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-02-26 21:50:48 +00:00
parent 30eb28886b
commit b69c2d0f70
3 changed files with 5 additions and 36 deletions
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8
java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java
View File

@ -48,12 +48,4 @@ public interface BAMFormatAwareShard extends Shard {
* @return An iterator over the reads stored in the shard.
*/
public StingSAMIterator iterator();
/**
* Get the bounds of the current shard. Current bounds
* will be the unfiltered extents of the current shard, from
* the start of the first interval to the end of the last interval.
* @return The bounds of the shard.
*/
public GenomeLoc getBounds();
}

12
java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java
View File

@ -86,14 +86,12 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
}
/**
* Get the bounds of the current shard. Current bounds
* will be the unfiltered extents of the current shard, from
* the start of the first interval to the end of the last interval.
* @return The bounds of the shard.
* returns the type of shard.
*/
public GenomeLoc getBounds() {
return null;
}
@Override
public ShardType getShardType() {
return shardType;
}
/**
* String representation of this shard.

21
java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java
View File

@ -95,27 +95,6 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
return chunks;
}
/**
* Get the bounds of the current shard. Current bounds
* will be the unfiltered extents of the current shard, from
* the start of the first interval to the end of the last interval.
* @return The bounds of the shard.
*/
public GenomeLoc getBounds() {
if(loci == null)
return null;
String contig = null;
long start = Long.MAX_VALUE, stop = 0;
for(GenomeLoc locus: loci) {
if(contig == null) contig = locus.getContig();
start = Math.min(locus.getStart(),start);
stop = Math.max(locus.getStop(),stop);
}
return GenomeLocParser.createGenomeLoc(contig,start,stop);
}
/**
* returns the type of shard.
*/