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Made the MergingSamIterator2 peekable. This iterator is being a ducktaped together swiss army knife, the iterators could use a redo soon. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@593 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-05-05 19:15:07 +00:00
parent 09b0b6b57d
commit daa2163ee8
2 changed files with 48 additions and 33 deletions
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29
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
import edu.mit.broad.picard.sam.SamFileHeaderMerger;
import edu.mit.broad.picard.util.PeekableIterator;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMReadGroupRecord;
@ -184,18 +183,11 @@ public class SAMDataSource implements SimpleDataSource {
SamFileHeaderMerger headerMerger = CreateHeader();
MergingSamRecordIterator2 iter = null;
/*if (false) { // !includeUnmappedReads) {
// make a merging iterator for this record
iter = new MergingSamRecordIterator2(headerMerger);
bound = fastMappedReadSeek(shard.getSize(), iter);
} else {*/
if (!intoUnmappedReads) {
// make a merging iterator for this record
iter = new MergingSamRecordIterator2(headerMerger);
//bound = unmappedReadSeek(shard.getSize(), iter);
bound = fastMappedReadSeek(shard.getSize(), iter);
bound = fastMappedReadSeek(shard.getSize(), iter);
}
if (bound == null || intoUnmappedReads) {
if (iter != null) {
@ -204,7 +196,6 @@ public class SAMDataSource implements SimpleDataSource {
iter = new MergingSamRecordIterator2(CreateHeader());
bound = toUnmappedReads(shard.getSize(), iter);
}
//}
if (bound == null) {
shard.signalDone();
@ -234,37 +225,35 @@ public class SAMDataSource implements SimpleDataSource {
private BoundedReadIterator toUnmappedReads(long readCount, MergingSamRecordIterator2 iter) throws SimpleDataSourceLoadException {
BoundedReadIterator bound;// is this the first time we're doing this?
int count = 0;
PeekableIterator<SAMRecord> peek = new PeekableIterator(iter);
// throw away as many reads as it takes
SAMRecord d = null;
while (peek.hasNext()) {
d = peek.peek();
while (iter.hasNext()) {
d = iter.peek();
int x = d.getReferenceIndex();
if (x < 0 || x >= d.getHeader().getSequenceDictionary().getSequences().size()) {
// we have the magic read that starts the unmapped read segment!
break;
}
peek.next();
iter.next();
}
// check to see what happened, did we run out of reads?
if (!peek.hasNext()) {
if (!iter.hasNext()) {
return null;
}
// now walk until we've taken the unmapped read count
while (peek.hasNext() && count < this.readsTaken) {
peek.next();
while (iter.hasNext() && count < this.readsTaken) {
iter.next();
}
// check to see what happened, did we run out of reads?
if (!peek.hasNext()) {
if (!iter.hasNext()) {
return null;
}
// we're good, increment our read cout
this.readsTaken += readCount;
return new BoundedReadIterator(peek, readCount);
return new BoundedReadIterator(iter, readCount);
}

52
java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
View File

@ -34,7 +34,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
protected final SamFileHeaderMerger samHeaderMerger;
protected final SAMFileHeader.SortOrder sortOrder;
protected static Logger logger = Logger.getLogger(MergingSamRecordIterator2.class);
private SAMRecord mNextRecord;
protected boolean initialized = false;
/**
@ -48,14 +48,11 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
}
/**
* this class MUST only be initialized once, since the creation of the
*/
/** this class MUST only be initialized once, since the creation of the */
private void lazyInitialization() {
if (initialized) {
throw new UnsupportedOperationException("You cannot double initialize a MergingSamRecordIterator2");
}
initialized = true;
final SAMRecordComparator comparator = getComparator();
for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
if (this.sortOrder != SAMFileHeader.SortOrder.unsorted && reader.getFileHeader().getSortOrder() != this.sortOrder) {
@ -65,9 +62,11 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, comparator);
addIfNotEmpty(iterator);
}
setInitialized();
}
public boolean supportsSeeking() {
public boolean supportsSeeking() {
return true;
}
@ -75,7 +74,6 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
if (initialized) {
throw new IllegalStateException("You cannot double initialize a MergingSamRecordIterator2");
}
initialized = true;
final SAMRecordComparator comparator = getComparator();
for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
@ -83,13 +81,14 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, recordIter, comparator);
addIfNotEmpty(iterator);
}
setInitialized();
}
public void query(final String contig, final int start, final int stop, final boolean contained) {
if (initialized) {
throw new IllegalStateException("You cannot double initialize a MergingSamRecordIterator2");
}
initialized = true;
final SAMRecordComparator comparator = getComparator();
for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
//reader.close();
@ -97,31 +96,57 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, recordIter, comparator);
addIfNotEmpty(iterator);
}
setInitialized();
}
public void queryContained(final String contig, final int start, final int stop) {
if (initialized) {
throw new IllegalStateException("You cannot double initialize a MergingSamRecordIterator2");
}
initialized = true;
final SAMRecordComparator comparator = getComparator();
for (final SAMFileReader reader : samHeaderMerger.getReaders()) {
Iterator<SAMRecord> recordIter = reader.queryContained(contig, start, stop);
final ComparableSamRecordIterator iterator = new ComparableSamRecordIterator(reader, recordIter, comparator);
addIfNotEmpty(iterator);
}
setInitialized();
}
private void setInitialized() {
initialized = true;
mNextRecord = nextRecord();
}
/** Returns true if any of the underlying iterators has more records, otherwise false. */
public boolean hasNext() {
if (!initialized) {
lazyInitialization();
}
return !this.pq.isEmpty();
if (this.pq.isEmpty() && mNextRecord == null) {
return false;
}
return true;
}
public SAMRecord next() {
SAMRecord r = mNextRecord;
if (!this.pq.isEmpty()) {
mNextRecord = nextRecord();
} else {
mNextRecord = null;
}
return r;
}
public SAMRecord peek() {
return mNextRecord;
}
/** Returns the next record from the top most iterator during merging. */
public SAMRecord next() {
public SAMRecord nextRecord() {
if (!initialized) {
lazyInitialization();
}
@ -147,7 +172,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
record.setAttribute(SAMTag.RG.toString(), readGroups.get(0).getReadGroupId());
record.setAttribute(SAMTag.SM.toString(), readGroups.get(0).getReadGroupId());
} else {
logger.warn("Unable to set read group of ungrouped read: unable to pick default group, there are " + readGroups.size() + " possible.");
logger.warn("Unable to set read group of ungrouped read: unable to pick default group, there are " + readGroups.size() + " possible.");
}
}
@ -222,7 +247,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
/**
* closes all the file handles for the readers....DO THIS or you will run out of handles
* with sharding.
* with sharding.
*/
public void close() {
for (SAMFileReader reader : samHeaderMerger.getReaders()) {
@ -233,6 +258,7 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
/**
* allows us to be used in the new style for loops
*
* @return
*/
public Iterator<SAMRecord> iterator() {