add test

hail-is · Mar 27, 2024 · d3e5ae7 · d3e5ae7
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diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/README.txt b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/README.txt
@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.128-705d4033e0c9
+  Created at 2024/03/27 12:03:10
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/_SUCCESS b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/_SUCCESS
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/README.txt b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/README.txt
@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.128-705d4033e0c9
+  Created at 2024/03/27 12:03:10
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/_SUCCESS b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/_SUCCESS
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/metadata.json.gz b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/metadata.json.gz
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/rows/metadata.json.gz b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/rows/metadata.json.gz
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/rows/parts/part-0 b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/cols/rows/parts/part-0
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/entries/README.txt b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/entries/README.txt
@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.128-705d4033e0c9
+  Created at 2024/03/27 12:03:10
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/entries/_SUCCESS b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/entries/_SUCCESS
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/entries/metadata.json.gz b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/entries/metadata.json.gz
diff --git a/...src/test/resources/sample.vcf-20-partitions-with-overlap.mt/entries/rows/metadata.json.gz b/...src/test/resources/sample.vcf-20-partitions-with-overlap.mt/entries/rows/metadata.json.gz
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-00-cdb826da-6c5c-47b6-945b-3190a87a6a14 b/...artitions-with-overlap.mt/entries/rows/parts/part-00-cdb826da-6c5c-47b6-945b-3190a87a6a14
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-01-06f6a507-61e2-4bd1-a917-e1809270144c b/...artitions-with-overlap.mt/entries/rows/parts/part-01-06f6a507-61e2-4bd1-a917-e1809270144c
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-02-881d024c-5baf-4fe6-bc8f-53eda3845bde b/...artitions-with-overlap.mt/entries/rows/parts/part-02-881d024c-5baf-4fe6-bc8f-53eda3845bde
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-03-1e085a57-4dcb-4131-bc79-353324ffad47 b/...artitions-with-overlap.mt/entries/rows/parts/part-03-1e085a57-4dcb-4131-bc79-353324ffad47
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-04-d17ed9aa-6b33-4b0b-85d5-578da32f7581 b/...artitions-with-overlap.mt/entries/rows/parts/part-04-d17ed9aa-6b33-4b0b-85d5-578da32f7581
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-05-40d512f8-23ba-485e-aefa-47eced2bfe6d b/...artitions-with-overlap.mt/entries/rows/parts/part-05-40d512f8-23ba-485e-aefa-47eced2bfe6d
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-06-9b2dc9c7-c8b1-4ed4-9056-20142b5f6658 b/...artitions-with-overlap.mt/entries/rows/parts/part-06-9b2dc9c7-c8b1-4ed4-9056-20142b5f6658
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-07-b9a32d97-cb10-4158-aeaa-645dcea68ca7 b/...artitions-with-overlap.mt/entries/rows/parts/part-07-b9a32d97-cb10-4158-aeaa-645dcea68ca7
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-08-c2a0123f-a3d4-4b80-9c21-73cb2bed0b63 b/...artitions-with-overlap.mt/entries/rows/parts/part-08-c2a0123f-a3d4-4b80-9c21-73cb2bed0b63
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-09-ca197aee-6bfd-4068-b771-e9ca63551a7c b/...artitions-with-overlap.mt/entries/rows/parts/part-09-ca197aee-6bfd-4068-b771-e9ca63551a7c
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-10-17048169-a98b-49ee-ae4d-62641023b3ac b/...artitions-with-overlap.mt/entries/rows/parts/part-10-17048169-a98b-49ee-ae4d-62641023b3ac
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-11-c89858f5-4d78-4739-af31-308a1c257ff4 b/...artitions-with-overlap.mt/entries/rows/parts/part-11-c89858f5-4d78-4739-af31-308a1c257ff4
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-12-3e391e78-782d-495d-a29c-cacc56e1baf8 b/...artitions-with-overlap.mt/entries/rows/parts/part-12-3e391e78-782d-495d-a29c-cacc56e1baf8
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-13-62566d28-e496-4538-a325-b567be66accf b/...artitions-with-overlap.mt/entries/rows/parts/part-13-62566d28-e496-4538-a325-b567be66accf
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-14-8ab32ab7-15cd-4302-bb45-6b3dc02db5b6 b/...artitions-with-overlap.mt/entries/rows/parts/part-14-8ab32ab7-15cd-4302-bb45-6b3dc02db5b6
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-15-c4301966-4fd8-4ea0-b439-b49a693bf683 b/...artitions-with-overlap.mt/entries/rows/parts/part-15-c4301966-4fd8-4ea0-b439-b49a693bf683
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-16-8d638c2e-b1a5-4507-ba00-337a02e3f431 b/...artitions-with-overlap.mt/entries/rows/parts/part-16-8d638c2e-b1a5-4507-ba00-337a02e3f431
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-17-0c739863-b5fe-4e33-8f47-3e2751b599df b/...artitions-with-overlap.mt/entries/rows/parts/part-17-0c739863-b5fe-4e33-8f47-3e2751b599df
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-18-35d65ae7-5d1d-43f8-bb21-e6565874975e b/...artitions-with-overlap.mt/entries/rows/parts/part-18-35d65ae7-5d1d-43f8-bb21-e6565874975e
diff --git a/...artitions-with-overlap.mt/entries/rows/parts/part-19-2fd81de2-5d34-43db-809d-2f1fe1e67200 b/...artitions-with-overlap.mt/entries/rows/parts/part-19-2fd81de2-5d34-43db-809d-2f1fe1e67200
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/README.txt b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/README.txt
@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.128-705d4033e0c9
+  Created at 2024/03/27 12:03:10
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/_SUCCESS b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/_SUCCESS
diff --git a/.../test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/globals/metadata.json.gz b/.../test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/globals/metadata.json.gz
diff --git a/.../src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/globals/parts/part-0 b/.../src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/globals/parts/part-0
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/metadata.json.gz b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/metadata.json.gz
diff --git a/...src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/rows/metadata.json.gz b/...src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/rows/metadata.json.gz
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/rows/parts/part-0 b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/globals/rows/parts/part-0
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/metadata.json.gz b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/metadata.json.gz
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/README.txt b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/README.txt
@@ -0,0 +1,3 @@
+This folder comprises a Hail (www.hail.is) native Table or MatrixTable.
+  Written with version 0.2.128-705d4033e0c9
+  Created at 2024/03/27 12:03:10
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/_SUCCESS b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/_SUCCESS
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/metadata.json b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/metadata.json
@@ -0,0 +1 @@
+{"file_version":67328,"hail_version":"0.2.128-705d4033e0c9","references_rel_path":"../references","table_type":"Table{global:Struct{},key:[locus],row:Struct{locus:Locus(GRCh37),alleles:Array[String],rsid:String,qual:Float64,filters:Set[String],info:Struct{NEGATIVE_TRAIN_SITE:Boolean,HWP:Float64,AC:Array[Int32],culprit:String,MQ0:Int32,ReadPosRankSum:Float64,AN:Int32,InbreedingCoeff:Float64,AF:Array[Float64],GQ_STDDEV:Float64,FS:Float64,DP:Int32,GQ_MEAN:Float64,POSITIVE_TRAIN_SITE:Boolean,VQSLOD:Float64,ClippingRankSum:Float64,BaseQRankSum:Float64,MLEAF:Array[Float64],MLEAC:Array[Int32],MQ:Float64,QD:Float64,END:Int32,DB:Boolean,HaplotypeScore:Float64,MQRankSum:Float64,CCC:Int32,NCC:Int32,DS:Boolean}}}","components":{"globals":{"name":"RVDComponentSpec","rel_path":"../globals/rows"},"rows":{"name":"RVDComponentSpec","rel_path":"rows"},"partition_counts":{"name":"PartitionCountsComponentSpec","counts":[18,17,17,18,17,17,17,18,17,17,17,18,17,17,17,18,17,17,17,18]},"properties":{"name":"PropertiesSpec","properties":{"distinctlyKeyed":false}}},"name":"TableSpec"}
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/metadata.json.gz b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/metadata.json.gz
diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/rows/metadata.json b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/rows/metadata.json
@@ -0,0 +1 @@
+{"name":"IndexedRVDSpec2","_key":["locus"],"_codecSpec":{"name":"TypedCodecSpec","_eType":"+EBaseStruct{locus:EBaseStruct{contig:+EBinary,position:+EInt32},alleles:EArray[EBinary],rsid:EBinary,qual:EFloat64,filters:EArray[EBinary],info:EBaseStruct{NEGATIVE_TRAIN_SITE:EBoolean,HWP:EFloat64,AC:EArray[EInt32],culprit:EBinary,MQ0:EInt32,ReadPosRankSum:EFloat64,AN:EInt32,InbreedingCoeff:EFloat64,AF:EArray[EFloat64],GQ_STDDEV:EFloat64,FS:EFloat64,DP:EInt32,GQ_MEAN:EFloat64,POSITIVE_TRAIN_SITE:EBoolean,VQSLOD:EFloat64,ClippingRankSum:EFloat64,BaseQRankSum:EFloat64,MLEAF:EArray[EFloat64],MLEAC:EArray[EInt32],MQ:EFloat64,QD:EFloat64,END:EInt32,DB:EBoolean,HaplotypeScore:EFloat64,MQRankSum:EFloat64,CCC:EInt32,NCC:EInt32,DS:EBoolean}}","_vType":"Struct{locus:Locus(GRCh37),alleles:Array[String],rsid:String,qual:Float64,filters:Set[String],info:Struct{NEGATIVE_TRAIN_SITE:Boolean,HWP:Float64,AC:Array[Int32],culprit:String,MQ0:Int32,ReadPosRankSum:Float64,AN:Int32,InbreedingCoeff:Float64,AF:Array[Float64],GQ_STDDEV:Float64,FS:Float64,DP:Int32,GQ_MEAN:Float64,POSITIVE_TRAIN_SITE:Boolean,VQSLOD:Float64,ClippingRankSum:Float64,BaseQRankSum:Float64,MLEAF:Array[Float64],MLEAC:Array[Int32],MQ:Float64,QD:Float64,END:Int32,DB:Boolean,HaplotypeScore:Float64,MQRankSum:Float64,CCC:Int32,NCC:Int32,DS:Boolean}}","_bufferSpec":{"name":"LEB128BufferSpec","child":{"name":"BlockingBufferSpec","blockSize":65536,"child":{"name":"ZstdBlockBufferSpec","blockSize":65536,"child":{"name":"StreamBlockBufferSpec"}}}}},"_indexSpec":{"name":"IndexSpec2","_relPath":"../../index","_leafCodec":{"name":"TypedCodecSpec","_eType":"EBaseStruct{first_idx:+EInt64,keys:+EArray[+EBaseStruct{key:+EBaseStruct{locus:EBaseStruct{contig:+EBinary,position:+EInt32}},offset:+EInt64,annotation:+EBaseStruct{entries_offset:EInt64}}]}","_vType":"Struct{first_idx:Int64,keys:Array[Struct{key:Struct{locus:Locus(GRCh37)},offset:Int64,annotation:Struct{entries_offset:Int64}}]}","_bufferSpec":{"name":"LEB128BufferSpec","child":{"name":"BlockingBufferSpec","blockSize":65536,"child":{"name":"ZstdBlockBufferSpec","blockSize":65536,"child":{"name":"StreamBlockBufferSpec"}}}}},"_internalNodeCodec":{"name":"TypedCodecSpec","_eType":"EBaseStruct{children:+EArray[+EBaseStruct{index_file_offset:+EInt64,first_idx:+EInt64,first_key:+EBaseStruct{locus:EBaseStruct{contig:+EBinary,position:+EInt32}},first_record_offset:+EInt64,first_annotation:+EBaseStruct{entries_offset:EInt64}}]}","_vType":"Struct{children:Array[Struct{index_file_offset:Int64,first_idx:Int64,first_key:Struct{locus:Locus(GRCh37)},first_record_offset:Int64,first_annotation:Struct{entries_offset:Int64}}]}","_bufferSpec":{"name":"LEB128BufferSpec","child":{"name":"BlockingBufferSpec","blockSize":65536,"child":{"name":"ZstdBlockBufferSpec","blockSize":65536,"child":{"name":"StreamBlockBufferSpec"}}}}},"_keyType":"Struct{locus:Locus(GRCh37)}","_annotationType":"Struct{entries_offset:Int64}"},"_partFiles":["part-00-cdb826da-6c5c-47b6-945b-3190a87a6a14","part-01-06f6a507-61e2-4bd1-a917-e1809270144c","part-02-881d024c-5baf-4fe6-bc8f-53eda3845bde","part-03-1e085a57-4dcb-4131-bc79-353324ffad47","part-04-d17ed9aa-6b33-4b0b-85d5-578da32f7581","part-05-40d512f8-23ba-485e-aefa-47eced2bfe6d","part-06-9b2dc9c7-c8b1-4ed4-9056-20142b5f6658","part-07-b9a32d97-cb10-4158-aeaa-645dcea68ca7","part-08-c2a0123f-a3d4-4b80-9c21-73cb2bed0b63","part-09-ca197aee-6bfd-4068-b771-e9ca63551a7c","part-10-17048169-a98b-49ee-ae4d-62641023b3ac","part-11-c89858f5-4d78-4739-af31-308a1c257ff4","part-12-3e391e78-782d-495d-a29c-cacc56e1baf8","part-13-62566d28-e496-4538-a325-b567be66accf","part-14-8ab32ab7-15cd-4302-bb45-6b3dc02db5b6","part-15-c4301966-4fd8-4ea0-b439-b49a693bf683","part-16-8d638c2e-b1a5-4507-ba00-337a02e3f431","part-17-0c739863-b5fe-4e33-8f47-3e2751b599df","part-18-35d65ae7-5d1d-43f8-bb21-e6565874975e","part-19-2fd81de2-5d34-43db-809d-2f1fe1e67200"],"_jRangeBounds":[{"start":{"locus":{"contig":"20","position":10019093}},"end":{"locus":{"contig":"20","position":10286773}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":10286773}},"end":{"locus":{"contig":"20","position":10603326}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":10603326}},"end":{"locus":{"contig":"20","position":10625804}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":10625804}},"end":{"locus":{"contig":"20","position":10653469}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":10653469}},"end":{"locus":{"contig":"20","position":13071871}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":13071871}},"end":{"locus":{"contig":"20","position":13260252}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":13260252}},"end":{"locus":{"contig":"20","position":13561632}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":13561632}},"end":{"locus":{"contig":"2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diff --git a/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/rows/metadata.json.gz b/hail/src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows/rows/metadata.json.gz
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-00-cdb826da-6c5c-47b6-945b-3190a87a6a14 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-00-cdb826da-6c5c-47b6-945b-3190a87a6a14
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-01-06f6a507-61e2-4bd1-a917-e1809270144c b/...0-partitions-with-overlap.mt/rows/rows/parts/part-01-06f6a507-61e2-4bd1-a917-e1809270144c
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-02-881d024c-5baf-4fe6-bc8f-53eda3845bde b/...0-partitions-with-overlap.mt/rows/rows/parts/part-02-881d024c-5baf-4fe6-bc8f-53eda3845bde
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-03-1e085a57-4dcb-4131-bc79-353324ffad47 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-03-1e085a57-4dcb-4131-bc79-353324ffad47
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-04-d17ed9aa-6b33-4b0b-85d5-578da32f7581 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-04-d17ed9aa-6b33-4b0b-85d5-578da32f7581
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-05-40d512f8-23ba-485e-aefa-47eced2bfe6d b/...0-partitions-with-overlap.mt/rows/rows/parts/part-05-40d512f8-23ba-485e-aefa-47eced2bfe6d
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-06-9b2dc9c7-c8b1-4ed4-9056-20142b5f6658 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-06-9b2dc9c7-c8b1-4ed4-9056-20142b5f6658
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-07-b9a32d97-cb10-4158-aeaa-645dcea68ca7 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-07-b9a32d97-cb10-4158-aeaa-645dcea68ca7
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-08-c2a0123f-a3d4-4b80-9c21-73cb2bed0b63 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-08-c2a0123f-a3d4-4b80-9c21-73cb2bed0b63
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-09-ca197aee-6bfd-4068-b771-e9ca63551a7c b/...0-partitions-with-overlap.mt/rows/rows/parts/part-09-ca197aee-6bfd-4068-b771-e9ca63551a7c
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-10-17048169-a98b-49ee-ae4d-62641023b3ac b/...0-partitions-with-overlap.mt/rows/rows/parts/part-10-17048169-a98b-49ee-ae4d-62641023b3ac
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-11-c89858f5-4d78-4739-af31-308a1c257ff4 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-11-c89858f5-4d78-4739-af31-308a1c257ff4
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-12-3e391e78-782d-495d-a29c-cacc56e1baf8 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-12-3e391e78-782d-495d-a29c-cacc56e1baf8
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-13-62566d28-e496-4538-a325-b567be66accf b/...0-partitions-with-overlap.mt/rows/rows/parts/part-13-62566d28-e496-4538-a325-b567be66accf
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-14-8ab32ab7-15cd-4302-bb45-6b3dc02db5b6 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-14-8ab32ab7-15cd-4302-bb45-6b3dc02db5b6
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-15-c4301966-4fd8-4ea0-b439-b49a693bf683 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-15-c4301966-4fd8-4ea0-b439-b49a693bf683
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-16-8d638c2e-b1a5-4507-ba00-337a02e3f431 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-16-8d638c2e-b1a5-4507-ba00-337a02e3f431
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-17-0c739863-b5fe-4e33-8f47-3e2751b599df b/...0-partitions-with-overlap.mt/rows/rows/parts/part-17-0c739863-b5fe-4e33-8f47-3e2751b599df
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-18-35d65ae7-5d1d-43f8-bb21-e6565874975e b/...0-partitions-with-overlap.mt/rows/rows/parts/part-18-35d65ae7-5d1d-43f8-bb21-e6565874975e
diff --git a/...0-partitions-with-overlap.mt/rows/rows/parts/part-19-2fd81de2-5d34-43db-809d-2f1fe1e67200 b/...0-partitions-with-overlap.mt/rows/rows/parts/part-19-2fd81de2-5d34-43db-809d-2f1fe1e67200
diff --git a/hail/src/test/scala/is/hail/expr/ir/TableIRSuite.scala b/hail/src/test/scala/is/hail/expr/ir/TableIRSuite.scala
@@ -7,12 +7,12 @@ import is.hail.annotations.SafeNDArray
 import is.hail.expr.Nat
 import is.hail.expr.ir.TestUtils._
 import is.hail.expr.ir.lowering.{DArrayLowering, LowerTableIR}
-import is.hail.methods.ForceCountTable
+import is.hail.methods.{ForceCountTable, NPartitionsTable}
 import is.hail.rvd.RVDPartitioner
 import is.hail.types._
 import is.hail.types.virtual._
 import is.hail.utils._
-
+import is.hail.variant.Locus
 import org.apache.spark.sql.Row
 import org.scalatest.{Failed, Succeeded}
 import org.scalatest.Inspectors.forAll
@@ -674,6 +674,25 @@ class TableIRSuite extends HailSuite {
     assertEvalsTo(TableCount(join), 346L)
   }
 
+  @Test def testNativeReaderWithOverlappingPartitions(): Unit = {
+    val path = "src/test/resources/sample.vcf-20-partitions-with-overlap.mt/rows"
+    // i1 overlaps the first two partitions
+    val i1 = Interval(Row(Locus("20", 10200000)), Row(Locus("20", 10500000)), true, true)
+
+    def test(filterIntervals: Boolean, expectedNParts: Int): Unit = {
+      val opts = NativeReaderOptions(FastSeq(i1), TLocus("GRCh37"), filterIntervals)
+      val tr = TableNativeReader(fs, TableNativeReaderParameters(path, Some(opts)))
+      val tir = TableRead(tr.fullTypeWithoutUIDs, false, tr)
+      val nParts = TableToValueApply(tir, NPartitionsTable())
+      val count = TableToValueApply(tir, ForceCountTable())
+      assertEvalsTo(nParts, expectedNParts)
+      assertEvalsTo(count, 20L)
+    }
+
+    test(false, 1)
+    test(true, 2)
+  }
+
   @Test def testTableKeyBy(): Unit = {
     implicit val execStrats = ExecStrategy.interpretOnly
     val data = Array(Array("A", 1), Array("A", 2), Array("B", 1))
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		{"file_version":67328,"hail_version":"0.2.128-705d4033e0c9","references_rel_path":"../references","table_type":"Table{global:Struct{},key:[locus],row:Struct{locus:Locus(GRCh37),alleles:Array[String],rsid:String,qual:Float64,filters:Set[String],info:Struct{NEGATIVE_TRAIN_SITE:Boolean,HWP:Float64,AC:Array[Int32],culprit:String,MQ0:Int32,ReadPosRankSum:Float64,AN:Int32,InbreedingCoeff:Float64,AF:Array[Float64],GQ_STDDEV:Float64,FS:Float64,DP:Int32,GQ_MEAN:Float64,POSITIVE_TRAIN_SITE:Boolean,VQSLOD:Float64,ClippingRankSum:Float64,BaseQRankSum:Float64,MLEAF:Array[Float64],MLEAC:Array[Int32],MQ:Float64,QD:Float64,END:Int32,DB:Boolean,HaplotypeScore:Float64,MQRankSum:Float64,CCC:Int32,NCC:Int32,DS:Boolean}}}","components":{"globals":{"name":"RVDComponentSpec","rel_path":"../globals/rows"},"rows":{"name":"RVDComponentSpec","rel_path":"rows"},"partition_counts":{"name":"PartitionCountsComponentSpec","counts":[18,17,17,18,17,17,17,18,17,17,17,18,17,17,17,18,17,17,17,18]},"properties":{"name":"PropertiesSpec","properties":{"distinctlyKeyed":false}}},"name":"TableSpec"}
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		{"name":"IndexedRVDSpec2","_key":["locus"],"_codecSpec":{"name":"TypedCodecSpec","_eType":"+EBaseStruct{locus:EBaseStruct{contig:+EBinary,position:+EInt32},alleles:EArray[EBinary],rsid:EBinary,qual:EFloat64,filters:EArray[EBinary],info:EBaseStruct{NEGATIVE_TRAIN_SITE:EBoolean,HWP:EFloat64,AC:EArray[EInt32],culprit:EBinary,MQ0:EInt32,ReadPosRankSum:EFloat64,AN:EInt32,InbreedingCoeff:EFloat64,AF:EArray[EFloat64],GQ_STDDEV:EFloat64,FS:EFloat64,DP:EInt32,GQ_MEAN:EFloat64,POSITIVE_TRAIN_SITE:EBoolean,VQSLOD:EFloat64,ClippingRankSum:EFloat64,BaseQRankSum:EFloat64,MLEAF:EArray[EFloat64],MLEAC:EArray[EInt32],MQ:EFloat64,QD:EFloat64,END:EInt32,DB:EBoolean,HaplotypeScore:EFloat64,MQRankSum:EFloat64,CCC:EInt32,NCC:EInt32,DS:EBoolean}}","_vType":"Struct{locus:Locus(GRCh37),alleles:Array[String],rsid:String,qual:Float64,filters:Set[String],info:Struct{NEGATIVE_TRAIN_SITE:Boolean,HWP:Float64,AC:Array[Int32],culprit:String,MQ0:Int32,ReadPosRankSum:Float64,AN:Int32,InbreedingCoeff:Float64,AF:Array[Float64],GQ_STDDEV:Float64,FS:Float64,DP:Int32,GQ_MEAN:Float64,POSITIVE_TRAIN_SITE:Boolean,VQSLOD:Float64,ClippingRankSum:Float64,BaseQRankSum:Float64,MLEAF:Array[Float64],MLEAC:Array[Int32],MQ:Float64,QD:Float64,END:Int32,DB:Boolean,HaplotypeScore:Float64,MQRankSum:Float64,CCC:Int32,NCC:Int32,DS:Boolean}}","_bufferSpec":{"name":"LEB128BufferSpec","child":{"name":"BlockingBufferSpec","blockSize":65536,"child":{"name":"ZstdBlockBufferSpec","blockSize":65536,"child":{"name":"StreamBlockBufferSpec"}}}}},"_indexSpec":{"name":"IndexSpec2","_relPath":"../../index","_leafCodec":{"name":"TypedCodecSpec","_eType":"EBaseStruct{first_idx:+EInt64,keys:+EArray[+EBaseStruct{key:+EBaseStruct{locus:EBaseStruct{contig:+EBinary,position:+EInt32}},offset:+EInt64,annotation:+EBaseStruct{entries_offset:EInt64}}]}","_vType":"Struct{first_idx:Int64,keys:Array[Struct{key:Struct{locus:Locus(GRCh37)},offset:Int64,annotation:Struct{entries_offset:Int64}}]}","_bufferSpec":{"name":"LEB128BufferSpec","child":{"name":"BlockingBufferSpec","blockSize":65536,"child":{"name":"ZstdBlockBufferSpec","blockSize":65536,"child":{"name":"StreamBlockBufferSpec"}}}}},"_internalNodeCodec":{"name":"TypedCodecSpec","_eType":"EBaseStruct{children:+EArray[+EBaseStruct{index_file_offset:+EInt64,first_idx:+EInt64,first_key:+EBaseStruct{locus:EBaseStruct{contig:+EBinary,position:+EInt32}},first_record_offset:+EInt64,first_annotation:+EBaseStruct{entries_offset:EInt64}}]}","_vType":"Struct{children:Array[Struct{index_file_offset:Int64,first_idx:Int64,first_key:Struct{locus:Locus(GRCh37)},first_record_offset:Int64,first_annotation:Struct{entries_offset:Int64}}]}","_bufferSpec":{"name":"LEB128BufferSpec","child":{"name":"BlockingBufferSpec","blockSize":65536,"child":{"name":"ZstdBlockBufferSpec","blockSize":65536,"child":{"name":"StreamBlockBufferSpec"}}}}},"_keyType":"Struct{locus:Locus(GRCh37)}","_annotationType":"Struct{entries_offset:Int64}"},"_partFiles":["part-00-cdb826da-6c5c-47b6-945b-3190a87a6a14","part-01-06f6a507-61e2-4bd1-a917-e1809270144c","part-02-881d024c-5baf-4fe6-bc8f-53eda3845bde","part-03-1e085a57-4dcb-4131-bc79-353324ffad47","part-04-d17ed9aa-6b33-4b0b-85d5-578da32f7581","part-05-40d512f8-23ba-485e-aefa-47eced2bfe6d","part-06-9b2dc9c7-c8b1-4ed4-9056-20142b5f6658","part-07-b9a32d97-cb10-4158-aeaa-645dcea68ca7","part-08-c2a0123f-a3d4-4b80-9c21-73cb2bed0b63","part-09-ca197aee-6bfd-4068-b771-e9ca63551a7c","part-10-17048169-a98b-49ee-ae4d-62641023b3ac","part-11-c89858f5-4d78-4739-af31-308a1c257ff4","part-12-3e391e78-782d-495d-a29c-cacc56e1baf8","part-13-62566d28-e496-4538-a325-b567be66accf","part-14-8ab32ab7-15cd-4302-bb45-6b3dc02db5b6","part-15-c4301966-4fd8-4ea0-b439-b49a693bf683","part-16-8d638c2e-b1a5-4507-ba00-337a02e3f431","part-17-0c739863-b5fe-4e33-8f47-3e2751b599df","part-18-35d65ae7-5d1d-43f8-bb21-e6565874975e","part-19-2fd81de2-5d34-43db-809d-2f1fe1e67200"],"_jRangeBounds":[{"start":{"locus":{"contig":"20","position":10019093}},"end":{"locus":{"contig":"20","position":10286773}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":10286773}},"end":{"locus":{"contig":"20","position":10603326}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":10603326}},"end":{"locus":{"contig":"20","position":10625804}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":10625804}},"end":{"locus":{"contig":"20","position":10653469}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":10653469}},"end":{"locus":{"contig":"20","position":13071871}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":13071871}},"end":{"locus":{"contig":"20","position":13260252}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":13260252}},"end":{"locus":{"contig":"20","position":13561632}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":13561632}},"end":{"locus":{"contig":"20","position":13709115}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":13709115}},"end":{"locus":{"contig":"20","position":13798776}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":13798776}},"end":{"locus":{"contig":"20","position":14032627}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":14032627}},"end":{"locus":{"contig":"20","position":15948325}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":15948325}},"end":{"locus":{"contig":"20","position":16347823}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":16347823}},"end":{"locus":{"contig":"20","position":16410559}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":16410559}},"end":{"locus":{"contig":"20","position":17410116}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":17410116}},"end":{"locus":{"contig":"20","position":17475217}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":17475217}},"end":{"locus":{"contig":"20","position":17595540}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":17595540}},"end":{"locus":{"contig":"20","position":17600357}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":17600357}},"end":{"locus":{"contig":"20","position":17608348}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":17608348}},"end":{"locus":{"contig":"20","position":17705709}},"includeStart":true,"includeEnd":true},{"start":{"locus":{"contig":"20","position":17705709}},"end":{"locus":{"contig":"20","position":17970876}},"includeStart":true,"includeEnd":true}],"_attrs":{}}