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

Added ignore all filters options to VQSR walkers

This commit is contained in:
Ryan Poplin 2014-09-10 13:34:04 -04:00
parent 31cea25c36
commit 48252897b4
2 changed files with 6 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/ApplyRecalibration.java
View File

@ -146,6 +146,8 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
*/ */
@Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file", required=false) @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file", required=false)
private String[] IGNORE_INPUT_FILTERS = null; private String[] IGNORE_INPUT_FILTERS = null;
@Argument(fullName="ignore_all_filters", shortName="ignoreAllFilters", doc="If specified, the variant recalibrator will ignore all input filters. Useful to rerun the VQSR from a filtered output file.", required=false)
private boolean IGNORE_ALL_FILTERS = false;
@Argument(fullName="excludeFiltered", shortName="ef", doc="Don't output filtered loci after applying the recalibration", required=false) @Argument(fullName="excludeFiltered", shortName="ef", doc="Don't output filtered loci after applying the recalibration", required=false)
protected boolean EXCLUDE_FILTERED = false; protected boolean EXCLUDE_FILTERED = false;
@Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously.", required = false) @Argument(fullName = "mode", shortName = "mode", doc = "Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously.", required = false)
@ -246,7 +248,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
for( final VariantContext vc : VCs ) { for( final VariantContext vc : VCs ) {
if( VariantDataManager.checkVariationClass( vc, MODE ) && (vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters())) ) { if( VariantDataManager.checkVariationClass( vc, MODE ) && (IGNORE_ALL_FILTERS || vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
final VariantContext recalDatum = getMatchingRecalVC(vc, recals); final VariantContext recalDatum = getMatchingRecalVC(vc, recals);
if( recalDatum == null ) { if( recalDatum == null ) {

4
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -213,6 +213,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
*/ */
@Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the variant recalibrator will also use variants marked as filtered by the specified filter name in the input VCF file", required=false) @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the variant recalibrator will also use variants marked as filtered by the specified filter name in the input VCF file", required=false)
private String[] IGNORE_INPUT_FILTERS = null; private String[] IGNORE_INPUT_FILTERS = null;
@Argument(fullName="ignore_all_filters", shortName="ignoreAllFilters", doc="If specified, the variant recalibrator will ignore all input filters. Useful to rerun the VQSR from a filtered output file.", required=false)
private boolean IGNORE_ALL_FILTERS = false;
@Output(fullName="rscript_file", shortName="rscriptFile", doc="The output rscript file generated by the VQSR to aid in visualization of the input data and learned model", required=false, defaultToStdout=false) @Output(fullName="rscript_file", shortName="rscriptFile", doc="The output rscript file generated by the VQSR to aid in visualization of the input data and learned model", required=false, defaultToStdout=false)
private File RSCRIPT_FILE = null; private File RSCRIPT_FILE = null;
@ -323,7 +325,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
final ExpandingArrayList<VariantDatum> variants = new ExpandingArrayList<>(); final ExpandingArrayList<VariantDatum> variants = new ExpandingArrayList<>();
for( final VariantContext vc : tracker.getValues(rods, context.getLocation()) ) { for( final VariantContext vc : tracker.getValues(rods, context.getLocation()) ) {
if( vc != null && ( vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters()) ) ) { if( vc != null && ( IGNORE_ALL_FILTERS || vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters()) ) ) {
if( VariantDataManager.checkVariationClass( vc, VRAC.MODE ) ) { if( VariantDataManager.checkVariationClass( vc, VRAC.MODE ) ) {
final VariantDatum datum = new VariantDatum(); final VariantDatum datum = new VariantDatum();