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Final stage of renaming 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3696 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-06-30 21:39:07 +00:00
parent 6e7927a47d
commit 5f2b2d860e
3 changed files with 9 additions and 11 deletions
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6
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
View File

@ -193,11 +193,11 @@ public class VariantContextUtils {
String name = first.getName(); String name = first.getName();
GenomeLoc loc = first.getLocation(); GenomeLoc loc = first.getLocation();
Set<Allele> alleles = new HashSet<Allele>(); Set<Allele> alleles = new TreeSet<Allele>();
Map<String, Genotype> genotypes = new HashMap<String, Genotype>(); Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();
double negLog10PError = -1; double negLog10PError = -1;
Set<String> filters = new HashSet<String>(); Set<String> filters = new HashSet<String>();
Map<String, String> attributes = new HashMap<String, String>(); Map<String, String> attributes = new TreeMap<String, String>();
int depth = 0; int depth = 0;
// filtering values // filtering values

7
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
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@ -1,5 +1,5 @@
/* /*
* Copyright (c) 2010. * Copyright (c) 2010, The Broad Institute
* *
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * obtaining a copy of this software and associated documentation
@ -12,15 +12,14 @@
* *
* The above copyright notice and this permission notice shall be * The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software. * included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE. * OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.gatk.walkers.variantutils; package org.broadinstitute.sting.gatk.walkers.variantutils;

7
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
View File

@ -1,5 +1,5 @@
/* /*
* Copyright (c) 2010. * Copyright (c) 2010, The Broad Institute
* *
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * obtaining a copy of this software and associated documentation
@ -12,15 +12,14 @@
* *
* The above copyright notice and this permission notice shall be * The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software. * included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE. * OTHER DEALINGS IN THE SOFTWARE.
*/ */
package org.broadinstitute.sting.gatk.walkers.variantutils; package org.broadinstitute.sting.gatk.walkers.variantutils;