Ensure output files are sorted by chromosomes (#79)

Closes: #79
Related-Issue: #79
Projected-Results-Impact: require-revalidation

CHANGES.md

@@ -4,7 +4,7 @@
 
 - Writing out proper SV type for Dragen CNV (#76)
 - Adding support for depth of coverage annotation (#73)
-- Merge multiple input VCFs in annotate-svs with clustering (#75)
+- Ensure output files are sorted by chromosomes (#79)
 
 ## v0.26
 

pom.xml

@@ -24,7 +24,6 @@
 		<h2.version>1.4.197</h2.version>
 		<htsjdk.version>2.24.1</htsjdk.version>
 		<jannovar.version>0.41</jannovar.version>
-		<intervaltree.version>1.0.0</intervaltree.version>
 		<externalsortinginjava.version>0.6.1</externalsortinginjava.version>
 	</properties>
 

tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected

@@ -1,2 +1,2 @@
-release	chromosome	chromosome_no	bin	chromosome2	chromosome_no2	bin2	pe_orientation	start	end	start_ci_left	start_ci_right	end_ci_left	end_ci_right	case_id	set_id	sv_uuid	caller	sv_type	sv_sub_type	info	num_hom_alt	num_hom_ref	num_het	num_hemi_alt	num_hemi_ref	genotype
-GRCh37	22	22	89	22	22	89	3to5	17400000	17700000	-29	29	-29	29	.	.	UUID	EMBL.DELLYv1.1.3	DEL	DEL	{"""affectedCarriers""":0,"""backgroundCarriers""":0,"""unaffectedCarriers""":0}	0	2	1	0	0	{"""Case_1_father-N1-DNA1-WGS1""":{"""cn""":2,"""ft""":{"""LowQual"""},"""gq""":14,"""gt""":"""0/1""","""pec""":0,"""pev""":0,"""src""":34,"""srv""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":35,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":29,"""srv""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":67,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":32,"""srv""":1}}
+release	chromosome	chromosome_no	bin	chromosome2	chromosome_no2	bin2	pe_orientation	start	end	start_ci_left	start_ci_right	end_ci_left	end_ci_right	case_id	set_id	sv_uuid	caller	sv_type	sv_sub_type	info	num_hom_alt	num_hom_ref	num_het	num_hemi_alt	num_hemi_ref	genotype
+GRCh37	22	22	89	22	22	89	3to5	17400000	17700000	-29	29	-29	29	.	.	UUID	EMBL.DELLYv1.1.3	DEL	DEL	{"""affectedCarriers""":0,"""backgroundCarriers""":0,"""unaffectedCarriers""":0}	0	2	1	0	0	{"""Case_1_father-N1-DNA1-WGS1""":{"""cn""":2,"""ft""":{"""LowQual"""},"""gq""":14,"""gt""":"""0/1""","""pec""":0,"""pev""":0,"""src""":34,"""srv""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":35,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":29,"""srv""":2},"""Case_1_mother-N1-DNA1-WGS1""":{"""cn""":2,"""gq""":67,"""gt""":"""0/0""","""pec""":0,"""pev""":0,"""src""":32,"""srv""":1}}

varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsArgs.java

@@ -118,16 +118,6 @@ public final class AnnotateSvsArgs {
           "Annotate CNV with coverage and mapping quality from maelstrom-core coverage VCF file")
   private List<String> coverageVcfs = new ArrayList<>();
 
-  @Parameter(
-      names = "--merge-overlap",
-      description = "Reciprocal overlap to require for merging (default: 0.75)")
-  private double mergeOverlap = 0.75;
-
-  @Parameter(
-      names = "--merge-bnd-radius",
-      description = "Merge BNDs within the given radius (default: 50)")
-  private int mergeBndRadius = 50;
-
   public String getRefseqSerPath() {
     return refseqSerPath;
   }
@@ -208,14 +198,6 @@ public List<String> getCoverageVcfs() {
     return coverageVcfs;
   }
 
-  public double getMergeOverlap() {
-    return mergeOverlap;
-  }
-
-  public int getMergeBndRadius() {
-    return mergeBndRadius;
-  }
-
   @Override
   public String toString() {
     return "AnnotateSvsArgs{"
@@ -277,10 +259,6 @@ public String toString() {
         + '\''
         + ", coverageVcfs="
         + coverageVcfs
-        + ", mergeOverlap="
-        + mergeOverlap
-        + ", mergeBndRadius="
-        + mergeBndRadius
         + '}';
   }
 }

varfish-annotator-core/pom.xml

@@ -25,12 +25,6 @@
 			<version>${htsjdk.version}</version>
 		</dependency>
 
-		<dependency>
-			<groupId>com.lodborg</groupId>
-			<artifactId>interval-tree</artifactId>
-			<version>${intervaltree.version}</version>
-		</dependency>
-
 		<dependency>
 			<groupId>com.google.code.externalsortinginjava</groupId>
 			<artifactId>externalsortinginjava</artifactId>