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Contracts for HasGenomeLocation. BAQ iterator variables are all final. Contracts added 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5844 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-05-23 02:21:59 +00:00
parent 43057bd15c
commit b814f4bbd6
2 changed files with 17 additions and 5 deletions
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3
java/src/org/broadinstitute/sting/utils/HasGenomeLocation.java
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@ -1,8 +1,11 @@
package org.broadinstitute.sting.utils; package org.broadinstitute.sting.utils;
import com.google.java.contract.Ensures;
/** /**
* Indicates that this object has a genomic location and provides a systematic interface to get it. * Indicates that this object has a genomic location and provides a systematic interface to get it.
*/ */
public interface HasGenomeLocation { public interface HasGenomeLocation {
@Ensures("result != null")
public GenomeLoc getLocation(); public GenomeLoc getLocation();
} }

19
java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.utils.baq; package org.broadinstitute.sting.utils.baq;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.picard.reference.IndexedFastaSequenceFile; import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
@ -12,11 +14,11 @@ import java.util.Iterator;
* Simple iterator that applies Heng's BAQ calculation to a stream of incoming reads * Simple iterator that applies Heng's BAQ calculation to a stream of incoming reads
*/ */
public class BAQSamIterator implements StingSAMIterator { public class BAQSamIterator implements StingSAMIterator {
StingSAMIterator it; private final StingSAMIterator it;
BAQ baqHMM = new BAQ(); // creates a BAQ creator with default parameters private final BAQ baqHMM = new BAQ(); // creates a BAQ creator with default parameters
IndexedFastaSequenceFile refReader = null; private final IndexedFastaSequenceFile refReader;
BAQ.CalculationMode cmode; private final BAQ.CalculationMode cmode;
BAQ.QualityMode qmode; private final BAQ.QualityMode qmode;
/** /**
* Creates a new BAMSamIterator using the reference getter refReader and applies the BAM to the reads coming * Creates a new BAMSamIterator using the reference getter refReader and applies the BAM to the reads coming
@ -27,6 +29,11 @@ public class BAQSamIterator implements StingSAMIterator {
* @param cmode * @param cmode
* @param qmode * @param qmode
*/ */
@Requires({
"refReader != null",
"it != null",
"cmode != null" ,
"qmode != null"})
public BAQSamIterator(IndexedFastaSequenceFile refReader, StingSAMIterator it, BAQ.CalculationMode cmode, BAQ.QualityMode qmode) { public BAQSamIterator(IndexedFastaSequenceFile refReader, StingSAMIterator it, BAQ.CalculationMode cmode, BAQ.QualityMode qmode) {
if ( cmode == BAQ.CalculationMode.OFF) throw new ReviewedStingException("BUG: shouldn't create BAQSamIterator with calculation mode OFF"); if ( cmode == BAQ.CalculationMode.OFF) throw new ReviewedStingException("BUG: shouldn't create BAQSamIterator with calculation mode OFF");
if ( qmode == BAQ.QualityMode.DONT_MODIFY ) throw new ReviewedStingException("BUG: shouldn't create BAQSamIterator with quailty mode DONT_MODIFY"); if ( qmode == BAQ.QualityMode.DONT_MODIFY ) throw new ReviewedStingException("BUG: shouldn't create BAQSamIterator with quailty mode DONT_MODIFY");
@ -37,6 +44,8 @@ public class BAQSamIterator implements StingSAMIterator {
this.qmode = qmode; this.qmode = qmode;
} }
@Requires("hasNext()")
@Ensures("result != null")
public SAMRecord next() { public SAMRecord next() {
//System.out.printf("BAQing during input%n"); //System.out.printf("BAQing during input%n");
SAMRecord read = it.next(); SAMRecord read = it.next();