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Minor cleanup of SAMDataSource as part of my system review 

-- Changed a few function from public to protected, as they are only used by the package contents, to simplify the SAMDataSource interface
This commit is contained in:
Mark DePristo 2012-11-30 15:04:33 -05:00
parent 66bbe46e5b
commit 8020ba14db
1 changed files with 3 additions and 5 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
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@ -30,12 +30,10 @@ import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import net.sf.samtools.util.RuntimeIOException; import net.sf.samtools.util.RuntimeIOException;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.downsampling.*;
import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
import org.broadinstitute.sting.gatk.downsampling.DownsamplingMethod;
import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadMetrics;
import org.broadinstitute.sting.gatk.ReadProperties; import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.downsampling.*;
import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.iterators.*; import org.broadinstitute.sting.gatk.iterators.*;
@ -567,7 +565,7 @@ public class SAMDataSource {
* *
* @return the start positions of the first chunk of reads for all BAM files * @return the start positions of the first chunk of reads for all BAM files
*/ */
public Map<SAMReaderID, GATKBAMFileSpan> getInitialReaderPositions() { protected Map<SAMReaderID, GATKBAMFileSpan> getInitialReaderPositions() {
Map<SAMReaderID, GATKBAMFileSpan> initialPositions = new HashMap<SAMReaderID, GATKBAMFileSpan>(); Map<SAMReaderID, GATKBAMFileSpan> initialPositions = new HashMap<SAMReaderID, GATKBAMFileSpan>();
SAMReaders readers = resourcePool.getAvailableReaders(); SAMReaders readers = resourcePool.getAvailableReaders();
@ -585,7 +583,7 @@ public class SAMDataSource {
* @param shard The shard specifying the data limits. * @param shard The shard specifying the data limits.
* @return An iterator over the selected data. * @return An iterator over the selected data.
*/ */
public StingSAMIterator getIterator( Shard shard ) { protected StingSAMIterator getIterator( Shard shard ) {
return getIterator(resourcePool.getAvailableReaders(), shard, shard instanceof ReadShard); return getIterator(resourcePool.getAvailableReaders(), shard, shard instanceof ReadShard);
} }