@Override public void close() { if (lastRecord != null) { lastRecord.detachFromIterator(); lastRecord = null; } alignedIterator = null; } }
@Override public void close() { if (lastRecord != null) { lastRecord.detachFromIterator(); lastRecord = null; } alignedIterator = null; } }
@Override public boolean hasNext() { // check unaligned if (hasMoreUnalignedFragments == null) { try { lastRecord.detachFromIterator(); nextUnalignedFragment(); } catch (ErrorMsg e) { throw new RuntimeException(e); } } return hasMoreUnalignedFragments; }
@Override public boolean hasNext() { // check unaligned if (hasMoreUnalignedFragments == null) { try { lastRecord.detachFromIterator(); nextUnalignedFragment(); } catch (ErrorMsg e) { throw new RuntimeException(e); } } return hasMoreUnalignedFragments; }
/** * Performs a deep copy of the SAMRecord and detaches a copy from NGS iterator * @return new object * @throws CloneNotSupportedException */ @Override public Object clone() throws CloneNotSupportedException { SRALazyRecord newObject = (SRALazyRecord)super.clone(); newObject.initializedFields = EnumSet.copyOf(this.initializedFields); newObject.initializedFlags = EnumSet.copyOf(this.initializedFlags); newObject.initializedAttributes = EnumSet.copyOf(this.initializedAttributes); newObject.detachFromIterator(); return newObject; }
/** * Performs a deep copy of the SAMRecord and detaches a copy from NGS iterator * @return new object * @throws CloneNotSupportedException */ @Override public Object clone() throws CloneNotSupportedException { SRALazyRecord newObject = (SRALazyRecord)super.clone(); newObject.initializedFields = EnumSet.copyOf(this.initializedFields); newObject.initializedFlags = EnumSet.copyOf(this.initializedFlags); newObject.initializedAttributes = EnumSet.copyOf(this.initializedAttributes); newObject.detachFromIterator(); return newObject; }
@Override public boolean hasNext() { // check aligned if (lastRecord != null) { lastRecord.detachFromIterator(); lastRecord = null; } if (hasMoreAlignments == null) { try { hasMoreAlignments = alignedIterator.nextAlignment(); } catch (ErrorMsg e) { throw new RuntimeException(e); } } while (!hasMoreAlignments && hasMoreReferences) { nextReference(); } return hasMoreAlignments; }
@Override public boolean hasNext() { // check aligned if (lastRecord != null) { lastRecord.detachFromIterator(); lastRecord = null; } if (hasMoreAlignments == null) { try { hasMoreAlignments = alignedIterator.nextAlignment(); } catch (ErrorMsg e) { throw new RuntimeException(e); } } while (!hasMoreAlignments && hasMoreReferences) { nextReference(); } return hasMoreAlignments; }