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Nway out fixed: in this mode a special nwayout sam writer is instantiated and passed to constrained manager. All the dispatching of the reads into separate output sam streams is taken care by that writer, so no other special processing is needed at the realigner/manager level. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6020 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-06-20 19:35:26 +00:00
parent 600a6a43a6
commit 7c322780d3
1 changed files with 52 additions and 99 deletions
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151
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -51,6 +51,7 @@ import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
import org.broadinstitute.sting.utils.interval.NwayIntervalMergingIterator;
import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
@ -91,9 +92,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Argument(fullName="entropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false)
protected double MISMATCH_THRESHOLD = 0.15;
@Output(required=true, doc="Output bam")
@Output(required=false, doc="Output bam")
protected StingSAMFileWriter writer = null;
protected ConstrainedMateFixingManager manager = null;
protected SAMFileWriter writerToUse = null;
@Argument(fullName = "consensusDeterminationModel", shortName = "model", doc = "How should we determine the possible alternate consenses? -- in the order of least permissive to most permissive there is KNOWNS_ONLY (use only indels from known indels provided in RODs), USE_READS (additionally use indels already present in the original alignments of the reads), and USE_SW (additionally use 'Smith-Waterman' to generate alternate consenses). The default is USE_SW", required = false)
public ConsensusDeterminationModel consensusModel = ConsensusDeterminationModel.USE_SW;
@ -219,7 +221,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
private FileWriter statsOutput = null;
private FileWriter snpsOutput = null;
protected Map<SAMReaderID, ConstrainedMateFixingManager> nwayWriters = null;
//###protected Map<SAMReaderID, ConstrainedMateFixingManager> nwayWriters = null;
// debug info for lazy SW evaluation:
@ -227,8 +229,43 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
private long SWalignmentRuns = 0; // how many times (=for how many reads) we ran SW alignment
private long SWalignmentSuccess = 0; // how many SW alignments were "successful" (i.e. found a workable indel and resulted in non-null consensus)
private Map<String,String> loadFileNameMap(String mapFile) {
Map<String,String> fname_map = new HashMap<String,String>();
try {
XReadLines reader = new XReadLines(new File(mapFile),true);
for ( String line : reader ) {
if ( line.length() == 0 ) continue;
String fields[] = line.split("\t");
if ( fields.length != 2 )
throw new UserException.BadInput("Input-output map file must have exactly two columns. Offending line:\n"+line);
if ( fields[0].length() == 0 || fields[1].length() == 0 )
throw new UserException.BadInput("Input-output map file can not have empty strings in either column. Offending line:\n"+line);
if ( fname_map.containsKey(fields[0]) )
throw new UserException.BadInput("Input-output map file contains duplicate entries for input name "+fields[0]);
if ( fname_map.containsValue(fields[1]) )
throw new UserException.BadInput("Input-output map file maps multiple entries onto single output name "+fields[1]);
fname_map.put(fields[0],fields[1]);
}
} catch (IOException e) {
throw new StingException("I/O Error while reading input-output map file "+N_WAY_OUT+": "+e.getMessage());
}
return fname_map;
}
public void initialize() {
if ( N_WAY_OUT == null && writer == null ) {
throw new UserException.CommandLineException("Either -o or -nWayOut must be specified");
}
if ( N_WAY_OUT != null && writer != null ) {
throw new UserException.CommandLineException("-o and -nWayOut can not be used simultaneously");
}
if ( LOD_THRESHOLD < 0.0 )
throw new RuntimeException("LOD threshold cannot be a negative number");
if ( MISMATCH_THRESHOLD <= 0.0 || MISMATCH_THRESHOLD > 1.0 )
@ -268,78 +305,22 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
currentInterval = intervals.hasNext() ? intervals.next() : null;
writerToUse = writer;
if ( N_WAY_OUT != null ) {
//if ( writer != null ) throw new UserException.BadInput("-nWayOut and -o arguments are mutually exclusive");
nwayWriters = new HashMap<SAMReaderID, ConstrainedMateFixingManager>();
Map<String,String> fname_map = null;
if ( N_WAY_OUT.toUpperCase().endsWith(".MAP") ) {
fname_map = new HashMap<String,String>();
try {
XReadLines reader = new XReadLines(new File(N_WAY_OUT),true);
for ( String line : reader ) {
if ( line.length() == 0 ) continue;
String fields[] = line.split("\t");
if ( fields.length != 2 )
throw new UserException.BadInput("Input-output map file must have exactly two columns. Offending line:\n"+line);
if ( fields[0].length() == 0 || fields[1].length() == 0 )
throw new UserException.BadInput("Input-output map file can not have empty strings in either column. Offending line:\n"+line);
if ( fname_map.containsKey(fields[0]) )
throw new UserException.BadInput("Input-output map file contains duplicate entries for input name "+fields[0]);
if ( fname_map.containsValue(fields[1]) )
throw new UserException.BadInput("Input-output map file maps multiple entries onto single output name "+fields[1]);
fname_map.put(fields[0],fields[1]);
}
} catch (IOException e) {
throw new StingException("I/O Error while reading input-output map file "+N_WAY_OUT+": "+e.getMessage());
}
writerToUse = new NWaySAMFileWriter(getToolkit(),loadFileNameMap(N_WAY_OUT),SAMFileHeader.SortOrder.coordinate,true);
} else {
writerToUse = new NWaySAMFileWriter(getToolkit(),N_WAY_OUT,SAMFileHeader.SortOrder.coordinate,true);
}
for ( SAMReaderID rid : getToolkit().getReadsDataSource().getReaderIDs() ) {
String fName = getToolkit().getReadsDataSource().getSAMFile(rid).getName();
String outName;
if ( fname_map != null ) {
if ( ! fname_map.containsKey(fName) )
throw new UserException.BadInput("Input-output map file does not contain an entry for the input file "+fName);
outName = fname_map.get(fName);
} else {
int pos ;
if ( fName.toUpperCase().endsWith(".BAM") ) pos = fName.toUpperCase().lastIndexOf(".BAM");
else {
if ( fName.toUpperCase().endsWith(".SAM") ) pos = fName.toUpperCase().lastIndexOf(".SAM");
else throw new UserException.BadInput("Input file name "+fName+" does not end with .sam or .bam");
}
String prefix = fName.substring(0,pos);
outName = prefix+N_WAY_OUT;
}
if ( nwayWriters.containsKey( rid ) )
throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
File f = new File(outName);
SAMFileHeader header = getToolkit().getSAMFileHeader(rid);
header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, f);
nwayWriters.put(rid, new ConstrainedMateFixingManager(sw, getToolkit().getGenomeLocParser(), MAX_ISIZE_FOR_MOVEMENT, MAX_POS_MOVE_ALLOWED, MAX_RECORDS_IN_MEMORY));
}
} else {
// set up the output writer
setupWriter(getToolkit().getSAMFileHeader());
}
// set up the output writer
setupWriter(getToolkit().getSAMFileHeader());
manager = new ConstrainedMateFixingManager(writer, getToolkit().getGenomeLocParser(), MAX_ISIZE_FOR_MOVEMENT, MAX_POS_MOVE_ALLOWED, MAX_RECORDS_IN_MEMORY);
manager = new ConstrainedMateFixingManager(writerToUse, getToolkit().getGenomeLocParser(), MAX_ISIZE_FOR_MOVEMENT, MAX_POS_MOVE_ALLOWED, MAX_RECORDS_IN_MEMORY);
if ( OUT_INDELS != null ) {
try {
@ -401,18 +382,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
boolean wasModified = readsActuallyCleaned.contains(read);
try {
if ( N_WAY_OUT != null ) {
SAMReaderID rid = getToolkit().getReaderIDForRead(read);
ConstrainedMateFixingManager m = nwayWriters.get(rid);
// reset read's read group from merged to original if read group id collision has happened in merging:
if ( getToolkit().getReadsDataSource().hasReadGroupCollisions() ) {
read.setAttribute("RG",
getToolkit().getReadsDataSource().getOriginalReadGroupId((String)read.getAttribute("RG")));
}
m.addRead(read, wasModified);
} else {
manager.addRead(read, wasModified);
}
manager.addRead(read, wasModified);
} catch (RuntimeIOException e) {
throw new UserException.ErrorWritingBamFile(e.getMessage());
}
@ -422,16 +392,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
// pre-merge lists to sort them in preparation for constrained SAMFileWriter
readsNotToClean.addAll(readsToClean.getReads());
ReadUtils.coordinateSortReads(readsNotToClean);
if ( N_WAY_OUT == null ) {
manager.addReads(readsNotToClean, readsActuallyCleaned);
} else {
// in this case, it is possible to have the following scenario: the realigner gets permission to realign,
// the cache in the ConstrainedMateFixingManager gets filled up while emitting reads, and then the
// first-of-pair mates of realigned reads don't get fixed because they were flushed out of the queue too early.
// Since the N-way option is @hidden, I'm not interested in fixing this right now.
for ( SAMRecord read : readsNotToClean )
emit(read);
}
manager.addReads(readsNotToClean, readsActuallyCleaned);
readsToClean.clear();
readsNotToClean.clear();
readsActuallyCleaned.clear();
@ -570,16 +531,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
}
if ( N_WAY_OUT != null ) {
try {
for ( ConstrainedMateFixingManager m : nwayWriters.values() )
m.close();
} catch (RuntimeIOException e) {
throw new UserException.ErrorWritingBamFile(e.getMessage());
}
} else {
manager.close();
}
manager.close();
if ( N_WAY_OUT != null ) writerToUse.close();
if ( CHECKEARLY ) {
logger.info("SW alignments runs: "+SWalignmentRuns);