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For Sendu: add a hidden option to allow bams to come out unsorted. We've agreed to let him deal with sorting these puppies on his own. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4767 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-12-01 17:56:13 +00:00
parent 3afa841a6a
commit 7caf666f48
1 changed files with 13 additions and 14 deletions
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27
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -56,7 +56,6 @@ import org.broadinstitute.sting.utils.collections.Pair;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.io.FileReader;
import java.util.*;
/**
@ -83,10 +82,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Output(required=false, doc="Output bam")
protected StingSAMFileWriter writer = null;
@Argument(fullName="output",shortName="O",doc="Please use --out instead")
@Deprecated
protected String oldOArg;
@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;
@ -106,6 +101,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
"if this value is exceeded, realignment is not attempted and the reads are passed to the output file(s) as-is", required=false)
protected int MAX_READS = 20000;
@Hidden
@Argument(fullName="doNotSortEvenThoughItIsHighlyUnsafe", required=false,
doc="Should we not sort the final bam at all?")
protected boolean DO_NOT_SORT = false;
@Argument(fullName="sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", required=false,
doc="Should we sort the final bam in coordinate order even though it will be malformed because "+
"mate pairs of realigned reads will contain inaccurate information?")
@ -334,18 +334,17 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
private SAMFileHeader setupHeader(SAMFileHeader header) {
if ( SORT_IN_COORDINATE_ORDER )
header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
else
header.setSortOrder(SAMFileHeader.SortOrder.queryname);
return header;
}
private void setupWriter(SAMFileHeader header) {
if ( SORT_IN_COORDINATE_ORDER )
if ( DO_NOT_SORT )
header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
else if ( SORT_IN_COORDINATE_ORDER )
header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
else
header.setSortOrder(SAMFileHeader.SortOrder.queryname);
return header;
}
private void setupWriter(SAMFileHeader header) {
header = setupHeader(header);
if ( !NO_PG_TAG ) {
final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);