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Reverting Matt's change from yesterday which I accidentally blew away when trying to cope with the stupid svn update issues we've been plagued with recently. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4495 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-14 14:40:42 +00:00
parent cfb33d8e12
commit 2606e67cf1
1 changed files with 77 additions and 0 deletions
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77
java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -1,8 +1,10 @@
package org.broadinstitute.sting.utils.sam;
import java.lang.reflect.Method;
import java.util.*;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
/**
@ -16,6 +18,11 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
* if they are ever modified externally then one must also invoke the
* setReadGroup() method here to ensure that the cache is kept up-to-date.
*
* 13 Oct 2010 - mhanna - this class is fundamentally flawed: it uses a decorator
* pattern to wrap a heavyweight object, which can lead
* to heinous side effects if the wrapping is not carefully
* done. Hopefully SAMRecord will become an interface and
* this will eventually be fixed.
*/
public class GATKSAMRecord extends SAMRecord {
@ -327,6 +334,76 @@ public class GATKSAMRecord extends SAMRecord {
public void setValidationStringency(net.sf.samtools.SAMFileReader.ValidationStringency validationStringency) { mRecord.setValidationStringency(validationStringency); }
public Object getAttribute(final String tag) { return mRecord.getAttribute(tag); }
public Integer getIntegerAttribute(final String tag) { return mRecord.getIntegerAttribute(tag); }
public Short getShortAttribute(final String tag) { return mRecord.getShortAttribute(tag); }
public Byte getByteAttribute(final String tag) { return mRecord.getByteAttribute(tag); }
public String getStringAttribute(final String tag) { return mRecord.getStringAttribute(tag); }
public Character getCharacterAttribute(final String tag) { return mRecord.getCharacterAttribute(tag); }
public Float getFloatAttribute(final String tag) { return mRecord.getFloatAttribute(tag); }
public byte[] getByteArrayAttribute(final String tag) { return mRecord.getByteArrayAttribute(tag); }
protected Object getAttribute(final short tag) {
Object attribute;
try {
Method method = mRecord.getClass().getDeclaredMethod("getAttribute",Short.TYPE);
method.setAccessible(true);
attribute = method.invoke(mRecord,tag);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke getAttribute method",ex);
}
return attribute;
}
public void setAttribute(final String tag, final Object value) { mRecord.setAttribute(tag,value); }
protected void setAttribute(final short tag, final Object value) {
try {
Method method = mRecord.getClass().getDeclaredMethod("setAttribute",Short.TYPE,Object.class);
method.setAccessible(true);
method.invoke(mRecord,tag,value);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke setAttribute method",ex);
}
}
public void clearAttributes() { mRecord.clearAttributes(); }
protected void setAttributes(final SAMBinaryTagAndValue attributes) {
try {
Method method = mRecord.getClass().getDeclaredMethod("setAttributes",SAMBinaryTagAndValue.class);
method.setAccessible(true);
method.invoke(mRecord,attributes);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke setAttributes method",ex);
}
}
protected SAMBinaryTagAndValue getBinaryAttributes() {
SAMBinaryTagAndValue binaryAttributes;
try {
Method method = mRecord.getClass().getDeclaredMethod("getBinaryAttributes");
method.setAccessible(true);
binaryAttributes = (SAMBinaryTagAndValue)method.invoke(mRecord);
}
catch(Exception ex) {
throw new ReviewedStingException("Unable to invoke getBinaryAttributes method",ex);
}
return binaryAttributes;
}
public List<SAMTagAndValue> getAttributes() { return mRecord.getAttributes(); }
public SAMFileHeader getHeader() { return mRecord.getHeader(); }
public void setHeader(SAMFileHeader samFileHeader) { mRecord.setHeader(samFileHeader); }