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The Indel Realigner now lets the engine do all of the setup for args affecting the SAM writer. Thanks, Matt! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4141 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-27 15:19:47 +00:00
parent a3d9d23b0f
commit 427a2f85e9
1 changed files with 7 additions and 26 deletions
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33
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.ReadWalker; import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.filters.BadMateFilter; import org.broadinstitute.sting.gatk.filters.BadMateFilter;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator; import org.broadinstitute.sting.utils.interval.IntervalFileMergingIterator;
import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.text.TextFormattingUtils;
@ -70,22 +71,15 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
protected double MISMATCH_THRESHOLD = 0.15; protected double MISMATCH_THRESHOLD = 0.15;
@Output(required=false, doc="Output bam") @Output(required=false, doc="Output bam")
protected String writerFilename = null; protected StingSAMFileWriter writer = null;
@Argument(fullName="output",shortName="O",doc="Please use --out instead") @Argument(fullName="output",shortName="O",doc="Please use --out instead")
@Deprecated @Deprecated
protected String oldOArg; protected String oldOArg;
@Argument(fullName="bam_compression", shortName="compress", required=false, doc="Compression level to use for output bams [default:5]")
protected Integer compressionLevel = 5;
@Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", required=false, doc="Don't run 'Smith-Waterman' to generate alternate consenses; use only known indels provided as RODs for constructing the alternate references.") @Argument(fullName="useOnlyKnownIndels", shortName="knownsOnly", required=false, doc="Don't run 'Smith-Waterman' to generate alternate consenses; use only known indels provided as RODs for constructing the alternate references.")
protected boolean USE_KNOWN_INDELS_ONLY = false; protected boolean USE_KNOWN_INDELS_ONLY = false;
@Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the SAMFileWriter. "+
"If too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool may run out of memory.", required=false)
protected int MAX_RECORDS_IN_RAM = 500000;
// ADVANCED OPTIONS FOLLOW // ADVANCED OPTIONS FOLLOW
@Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necessary to improve performance in deep coverage)", required=false) @Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necessary to improve performance in deep coverage)", required=false)
@ -141,9 +135,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
private final ArrayList<SAMRecord> readsNotToClean = new ArrayList<SAMRecord>(); private final ArrayList<SAMRecord> readsNotToClean = new ArrayList<SAMRecord>();
private final IdentityHashMap<Object, VariantContext> knownIndelsToTry = new IdentityHashMap<Object, VariantContext>(); private final IdentityHashMap<Object, VariantContext> knownIndelsToTry = new IdentityHashMap<Object, VariantContext>();
// the wrapper around the SAM writer
private SAMFileWriter writer = null;
// random number generator // random number generator
private static final long RANDOM_SEED = 1252863495; private static final long RANDOM_SEED = 1252863495;
private static final Random generator = new Random(RANDOM_SEED); private static final Random generator = new Random(RANDOM_SEED);
@ -187,14 +178,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
currentInterval = intervals.hasNext() ? intervals.next() : null; currentInterval = intervals.hasNext() ? intervals.next() : null;
// set up the output writer(s) // set up the output writer(s)
if ( writerFilename != null ) { if ( writer != null )
SAMFileWriterFactory factory = new SAMFileWriterFactory(); setupWriter(getToolkit().getSAMFileHeader());
factory.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
SAMFileHeader header = getToolkit().getSAMFileHeader();
File file = new File(writerFilename);
writer = makeWriter(factory, header, file);
}
if ( OUT_INDELS != null ) { if ( OUT_INDELS != null ) {
try { try {
@ -225,7 +210,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
} }
} }
private SAMFileWriter makeWriter(SAMFileWriterFactory factory, SAMFileHeader header, File file) { private void setupWriter(SAMFileHeader header) {
if ( SORT_IN_COORDINATE_ORDER ) if ( SORT_IN_COORDINATE_ORDER )
header.setSortOrder(SAMFileHeader.SortOrder.coordinate); header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
else else
@ -249,9 +234,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
header.setProgramRecords(newRecords); header.setProgramRecords(newRecords);
} }
SAMFileWriter writer = factory.makeBAMWriter(header, false, file, compressionLevel); writer.writeHeader(header);
writer.setPresorted(false);
return writer;
} }
private void emit(final SAMRecord read) { private void emit(final SAMRecord read) {
@ -371,9 +355,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
emit(readsNotToClean); emit(readsNotToClean);
} }
if ( writer != null )
writer.close();
if ( OUT_INDELS != null ) { if ( OUT_INDELS != null ) {
try { try {
indelOutput.close(); indelOutput.close();