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added a check of the sort ordering to the query methods, so that we detect if a file is unsorted much earlier. Also added some verbosity to the exception; it now contains an information about the raw attribute we saw for 'SO', the sort order of the bam file. 

Also fixed a bunch of documentation

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1015 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-15 22:15:03 +00:00
parent 2259dc3a8f
commit a0a549557f
1 changed files with 75 additions and 24 deletions
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99
java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
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@ -1,13 +1,28 @@
/*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever.
* Neither the Broad Institute nor MIT can be responsible for its use, misuse, or
* functionality.
*/
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.iterators;
import net.sf.picard.PicardException;
@ -38,28 +53,35 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
protected static Logger logger = Logger.getLogger(MergingSamRecordIterator2.class);
private SAMRecord mNextRecord;
protected boolean initialized = false;
protected final Reads reads;
/**
* Constructs a new merging iterator with the same set of readers and sort order as
* provided by the header merger parameter.
*
* @param headerMerger the header to merge
* @param reads the reads pile
*/
public MergingSamRecordIterator2(final SamFileHeaderMerger headerMerger, Reads reads) {
this.samHeaderMerger = headerMerger;
this.reads = reads;
this.sortOrder = headerMerger.getMergedHeader().getSortOrder();
this.pq = new PriorityQueue<ComparableSamRecordIterator>(samHeaderMerger.getReaders().size());
}
/** this class MUST only be initialized once, since the creation of the */
/**
* we hold off initializing because we don't know if they plan to query or just iterate. This function
* gets called if the hasNext() determines we haven't been query-ed yet, and we want to setup the iterator to start
* at the beginning of the read pile
*/
private void lazyInitialization() {
if (initialized) {
throw new UnsupportedOperationException("You cannot double initialize a MergingSamRecordIterator2");
}
final SAMRecordComparator comparator = getComparator();
for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
if (this.sortOrder != SAMFileHeader.SortOrder.unsorted && reader.getFileHeader().getSortOrder() != this.sortOrder) {
throw new PicardException("Files are not compatible with sort order: " + reader.getFileHeader().getSortOrder() + " vrs " + this.sortOrder);
}
checkSortOrder(reader);
final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, comparator);
addIfNotEmpty(iterator);
@ -68,6 +90,14 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
}
private void checkSortOrder(SAMFileReader reader) {
if (this.sortOrder != SAMFileHeader.SortOrder.unsorted && reader.getFileHeader().getSortOrder() != this.sortOrder) {
throw new PicardException("Files are not compatible with sort order: " + reader.getFileHeader().getSortOrder() +
" vrs " + this.sortOrder + ". Make sure that the SO flag in your bam file is set (The reader attribute for sort order equals "
+ reader.getFileHeader().getAttribute("SO") + " in this case).");
}
}
public boolean supportsSeeking() {
return true;
}
@ -79,6 +109,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
final SAMRecordComparator comparator = getComparator();
for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
checkSortOrder(reader);
Iterator<SAMRecord> recordIter = reader.queryOverlapping(contig, start, stop);
final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, recordIter, comparator);
addIfNotEmpty(iterator);
@ -93,6 +124,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
}
final SAMRecordComparator comparator = getComparator();
for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
checkSortOrder(reader);
Iterator<SAMRecord> recordIter = reader.query(contig, start, stop, contained);
final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, recordIter, comparator);
addIfNotEmpty(iterator);
@ -107,6 +139,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
}
final SAMRecordComparator comparator = getComparator();
for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
checkSortOrder(reader);
Iterator<SAMRecord> recordIter = reader.queryContained(contig, start, stop);
final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, recordIter, comparator);
addIfNotEmpty(iterator);
@ -142,11 +175,16 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
return r;
}
/** @return the next record, without moving the iterator */
public SAMRecord peek() {
return mNextRecord;
}
/** Returns the next record from the top most iterator during merging. */
/**
* Returns the next record from the top most iterator during merging.
*
* @return the next record, null if it's unavailable
*/
public SAMRecord nextRecord() {
if (!initialized) {
lazyInitialization();
@ -184,9 +222,9 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
record.setHeader(samHeaderMerger.getMergedHeader());
if (this.samHeaderMerger.hasMergedSequenceDictionary() && record.getReferenceIndex() >= 0) {
record.setReferenceIndex(this.samHeaderMerger.getMergedSequenceIndex(iterator.getReader(),record.getReferenceIndex()));
record.setReferenceIndex(this.samHeaderMerger.getMergedSequenceIndex(iterator.getReader(), record.getReferenceIndex()));
}
//System.out.printf("NEXT = %s %s %d%n", record.getReadName(), record.getReferenceName(), record.getAlignmentStart());
//System.out.printf("PEEK = %s %s %d%n", this.pq.peek().peek().getReadName(), this.pq.peek().peek().getReferenceName(), this.pq.peek().peek().getAlignmentStart());
@ -196,6 +234,8 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
/**
* Adds iterator to priority queue. If the iterator has more records it is added
* otherwise it is closed and not added.
*
* @param iterator the iterator to add
*/
protected void addIfNotEmpty(final ComparableSamRecordIterator iterator) {
//System.out.printf("Adding %s %s %d%n", iterator.peek().getReadName(), iterator.peek().getReferenceName(), iterator.peek().getAlignmentStart());
@ -215,6 +255,8 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
* Get the right comparator for a given sort order (coordinate, alphabetic). In the
* case of "unsorted" it will return a comparator that gives an arbitrary but reflexive
* ordering.
*
* @return the SAMRecordComparator appropriate for our sort order
*/
protected SAMRecordComparator getComparator() {
// For unsorted build a fake comparator that compares based on object ID
@ -249,7 +291,11 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
}
}
/** Returns the merged header that the merging iterator is working from. */
/**
* Returns the merged header that the merging iterator is working from.
*
* @return our sam file header
*/
public SAMFileHeader getHeader() {
return this.samHeaderMerger.getMergedHeader();
}
@ -260,7 +306,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
* with sharding.
*/
public void close() {
for( ComparableSamRecordIterator iterator: pq )
for (ComparableSamRecordIterator iterator : pq)
iterator.close();
}
@ -268,7 +314,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
/**
* allows us to be used in the new style for loops
*
* @return
* @return this iterator, which can be used in for loop each iterations
*/
public Iterator<SAMRecord> iterator() {
return this;
@ -278,10 +324,10 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
* Gets source information for the reads. Contains information about the original reads
* files, plus information about downsampling, etc.
*
* @return
* @return the read object we were created for
*/
public Reads getSourceInfo() {
return null; //To change body of implemented methods use File | Settings | File Templates.
return this.reads;
}
}
@ -312,12 +358,16 @@ class ComparableSamRecordIterator extends PeekableIterator<SAMRecord> implements
}
public Reads getSourceInfo() {
if( sourceInfo == null )
if (sourceInfo == null)
throw new StingException("Unable to provide source info for the reads. Please upgrade to the new data sharding framework.");
return sourceInfo;
}
}
/** Returns the reader from which this iterator was constructed. */
/**
* Returns the reader from which this iterator was constructed.
*
* @return the SAMFileReader
*/
public SAMFileReader getReader() {
return reader;
}
@ -328,6 +378,7 @@ class ComparableSamRecordIterator extends PeekableIterator<SAMRecord> implements
* comparator types internally an exception is thrown.
*
* @param that another iterator to compare to
*
* @return a negative, 0 or positive number as described in the Comparator interface
*/
public int compareTo(final ComparableSamRecordIterator that) {