zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Add a hidden mode to the realigner to turn off SW but still use indels other than known ones (i.e. those already in the reads) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4969 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-01-10 20:27:04 +00:00
parent 01c2091cd9
commit ee348ac9d4
1 changed files with 7 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -91,6 +91,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@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;
@Hidden
@Argument(fullName="doNotUseSW", shortName="doNotUseSW", required=false, doc="Don't run 'Smith-Waterman' to generate alternate consenses; use only known indels provided as RODs or indels in the reads for constructing the alternate references.")
protected boolean NO_SW = 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;
@ -598,10 +602,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
byte[] reference = readsToClean.getReference(referenceReader);
int leftmostIndex = (int)readsToClean.getLocation().getStart();
final ArrayList<SAMRecord> refReads = new ArrayList<SAMRecord>(); // reads that perfectly match ref
final ArrayList<SAMRecord> refReads = new ArrayList<SAMRecord>(); // reads that perfectly match ref
final ArrayList<AlignedRead> altReads = new ArrayList<AlignedRead>(); // reads that don't perfectly match
final LinkedList<AlignedRead> altAlignmentsToTest = new LinkedList<AlignedRead>(); // should we try to make an alt consensus from the read?
final Set<Consensus> altConsenses = new LinkedHashSet<Consensus>(); // list of alt consenses
final Set<Consensus> altConsenses = new LinkedHashSet<Consensus>(); // list of alt consenses
// if there are any known indels for this region, get them and create alternate consenses
generateAlternateConsensesFromKnownIndels(altConsenses, leftmostIndex, reference);
@ -611,7 +615,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
long totalRawMismatchSum = determineReadsThatNeedCleaning(reads, refReads, altReads, altAlignmentsToTest, altConsenses, leftmostIndex, reference);
// use 'Smith-Waterman' to create alternate consenses from reads that mismatch the reference, using totalRawMismatchSum as the random seed
if ( !USE_KNOWN_INDELS_ONLY )
if ( !USE_KNOWN_INDELS_ONLY && !NO_SW )
generateAlternateConsensesFromReads(altAlignmentsToTest, altConsenses, reference, leftmostIndex, totalRawMismatchSum);
// if ( debugOn ) System.out.println("------\nChecking consenses...\n--------\n");