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Default logic (and name) has changed. Now somatic mode is default one. In order to run in single-sample (unpaired) mode, one has to use (hidden) --unpaired option. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6022 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-06-21 17:08:41 +00:00
parent c5de06a641
commit 78461bac1e
1 changed files with 9 additions and 6 deletions
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15
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java → java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
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@ -72,7 +72,7 @@ import java.util.*;
* only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords. * only somatic calls, while --verbose output contains all calls annotated with GERMLINE/SOMATIC keywords.
*/ */
@ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, PlatformUnitFilter.class}) @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class, PlatformUnitFilter.class})
public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> { public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
// @Output // @Output
// PrintStream out; // PrintStream out;
@Output(doc="File to which variants should be written",required=true) @Output(doc="File to which variants should be written",required=true)
@ -101,9 +101,11 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
"to sort and keep it in memory (increases memory usage!).") "to sort and keep it in memory (increases memory usage!).")
protected boolean GENOTYPE_NOT_SORTED = false; protected boolean GENOTYPE_NOT_SORTED = false;
@Argument(fullName="somatic", shortName="somatic", @Hidden
doc="Perform somatic calls; two input alignment files (-I option) must be specified. Calls are performed from the second file (\"tumor\") against the first one (\"normal\").", required=false) @Argument(fullName="unpaired", shortName="unpaired",
boolean call_somatic = false; doc="Perform unpaired calls (no somatic status detection)", required=false)
boolean call_unpaired = false;
boolean call_somatic ;
@Argument(fullName="verboseOutput", shortName="verbose", @Argument(fullName="verboseOutput", shortName="verbose",
doc="Verbose output file in text format", required=false) doc="Verbose output file in text format", required=false)
@ -236,6 +238,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
@Override @Override
public void initialize() { public void initialize() {
call_somatic = (call_unpaired ? false : true);
normal_context = new WindowContext(0,WINDOW_SIZE); normal_context = new WindowContext(0,WINDOW_SIZE);
normalSamples = new HashSet<String>(); normalSamples = new HashSet<String>();
@ -263,7 +266,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
int nSams = getToolkit().getArguments().samFiles.size(); int nSams = getToolkit().getArguments().samFiles.size();
if ( call_somatic ) { if ( call_somatic ) {
if ( nSams < 2 ) throw new UserException.BadInput("At least two bam files (normal and tumor) must be specified in somatic mode"); if ( nSams < 2 ) throw new UserException.BadInput("In default (paired sample) mode at least two bam files (normal and tumor) must be specified");
tumor_context = new WindowContext(0,WINDOW_SIZE); tumor_context = new WindowContext(0,WINDOW_SIZE);
tumorSamples = new HashSet<String>(); tumorSamples = new HashSet<String>();
} }
@ -273,7 +276,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
for ( SAMReaderID rid : getToolkit().getReadsDataSource().getReaderIDs() ) { for ( SAMReaderID rid : getToolkit().getReadsDataSource().getReaderIDs() ) {
Tags tags = rid.getTags() ; Tags tags = rid.getTags() ;
if ( tags.getPositionalTags().isEmpty() && call_somatic ) if ( tags.getPositionalTags().isEmpty() && call_somatic )
throw new UserException.BadInput("In somatic mode all input bam files must be tagged as either 'normal' or 'tumor'. Untagged file: "+ throw new UserException.BadInput("In default (paired sample) mode all input bam files must be tagged as either 'normal' or 'tumor'. Untagged file: "+
getToolkit().getSourceFileForReaderID(rid)); getToolkit().getSourceFileForReaderID(rid));
boolean normal = false; boolean normal = false;
boolean tumor = false; boolean tumor = false;