API refactor

No longer using pysam.VariantFile and pysam.VariantRecord, but truvari.VariantFile and truvari.VariantRecord. These are simply wrappers around the pysam objects that exposes advanced functonality to facilitate comparison of entries.
ACEnglish · Jan 6, 2025 · a08f392 · a08f392
1 parent 4562a5a
commit a08f392
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Showing 60 changed files with 946 additions and 984 deletions.
diff --git a/repo_utils/answer_key/bench/bench12/fn.vcf.gz b/repo_utils/answer_key/bench/bench12/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12/log.txt b/repo_utils/answer_key/bench/bench12/log.txt
@@ -1,6 +1,6 @@
-2025-01-06 03:03:52,435 [INFO] Truvari v5.0.0
-2025-01-06 03:03:52,435 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench12/
-2025-01-06 03:03:52,436 [INFO] Params:
+2025-01-06 19:48:51,838 [INFO] Truvari v5.0.0
+2025-01-06 19:48:51,838 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench12/
+2025-01-06 19:48:51,839 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz",
@@ -29,9 +29,9 @@
     "check_monref": true,
     "check_multi": true
 }
-2025-01-06 03:03:52,680 [INFO] Zipped 3936 variants Counter({'base': 2153, 'comp': 1783})
-2025-01-06 03:03:52,681 [INFO] 12 chunks of 3936 variants Counter({'__filtered': 3904, 'base': 18, 'comp': 14})
-2025-01-06 03:03:52,717 [INFO] Stats: {
+2025-01-06 19:48:52,267 [INFO] Zipped 3936 variants Counter({'base': 2153, 'comp': 1783})
+2025-01-06 19:48:52,268 [INFO] 12 chunks of 3936 variants Counter({'__filtered': 3904, 'base': 18, 'comp': 14})
+2025-01-06 19:48:52,304 [INFO] Stats: {
     "TP-base": 8,
     "TP-comp": 8,
     "FP": 3,
@@ -62,4 +62,4 @@
         }
     }
 }
-2025-01-06 03:03:52,718 [INFO] Finished bench
+2025-01-06 19:48:52,304 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/log.txt b/repo_utils/answer_key/bench/bench12_gtcomp/log.txt
@@ -1,6 +1,6 @@
-2025-01-06 03:04:01,383 [INFO] Truvari v5.0.0
-2025-01-06 03:04:01,383 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench12_gtcomp/ --pick ac
-2025-01-06 03:04:01,384 [INFO] Params:
+2025-01-06 19:49:00,627 [INFO] Truvari v5.0.0
+2025-01-06 19:49:00,628 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench12_gtcomp/ --pick ac
+2025-01-06 19:49:00,628 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz",
@@ -29,9 +29,9 @@
     "check_monref": true,
     "check_multi": true
 }
-2025-01-06 03:04:01,649 [INFO] Zipped 3936 variants Counter({'base': 2153, 'comp': 1783})
-2025-01-06 03:04:01,650 [INFO] 12 chunks of 3936 variants Counter({'__filtered': 3904, 'base': 18, 'comp': 14})
-2025-01-06 03:04:01,689 [INFO] Stats: {
+2025-01-06 19:49:01,097 [INFO] Zipped 3936 variants Counter({'base': 2153, 'comp': 1783})
+2025-01-06 19:49:01,097 [INFO] 12 chunks of 3936 variants Counter({'__filtered': 3904, 'base': 18, 'comp': 14})
+2025-01-06 19:49:01,141 [INFO] Stats: {
     "TP-base": 9,
     "TP-comp": 8,
     "FP": 3,
@@ -62,4 +62,4 @@
         }
     }
 }
-2025-01-06 03:04:01,690 [INFO] Finished bench
+2025-01-06 19:49:01,141 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13/fn.vcf.gz b/repo_utils/answer_key/bench/bench13/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13/log.txt b/repo_utils/answer_key/bench/bench13/log.txt
@@ -1,6 +1,6 @@
-2025-01-06 03:03:53,974 [INFO] Truvari v5.0.0
-2025-01-06 03:03:53,975 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13/
-2025-01-06 03:03:53,975 [INFO] Params:
+2025-01-06 19:46:06,885 [INFO] Truvari v5.0.0
+2025-01-06 19:46:06,886 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13/
+2025-01-06 19:46:06,887 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz",
@@ -29,9 +29,9 @@
     "check_monref": true,
     "check_multi": true
 }
-2025-01-06 03:03:54,559 [INFO] Zipped 4218 variants Counter({'base': 2153, 'comp': 2065})
-2025-01-06 03:03:54,560 [INFO] 14 chunks of 4218 variants Counter({'__filtered': 4179, 'comp': 21, 'base': 18})
-2025-01-06 03:03:54,606 [INFO] Stats: {
+2025-01-06 19:46:07,352 [INFO] Zipped 4218 variants Counter({'base': 2153, 'comp': 2065})
+2025-01-06 19:46:07,353 [INFO] 14 chunks of 4218 variants Counter({'__filtered': 4179, 'comp': 21, 'base': 18})
+2025-01-06 19:46:07,392 [INFO] Stats: {
     "TP-base": 10,
     "TP-comp": 10,
     "FP": 7,
@@ -61,4 +61,4 @@
         }
     }
 }
-2025-01-06 03:03:54,607 [INFO] Finished bench
+2025-01-06 19:46:07,392 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz b/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_extend/log.txt b/repo_utils/answer_key/bench/bench13_extend/log.txt
@@ -1,6 +1,6 @@
-2025-01-06 03:03:58,792 [INFO] Truvari v5.0.0
-2025-01-06 03:03:58,793 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13_extend/ --includebed repo_utils/test_files/beds/include.bed --extend 500
-2025-01-06 03:03:58,794 [INFO] Params:
+2025-01-06 19:48:57,885 [INFO] Truvari v5.0.0
+2025-01-06 19:48:57,886 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13_extend/ --includebed repo_utils/test_files/beds/include.bed --extend 500
+2025-01-06 19:48:57,886 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz",
@@ -29,13 +29,13 @@
     "check_monref": true,
     "check_multi": true
 }
-2025-01-06 03:03:58,809 [INFO] Including 11 bed regions
-2025-01-06 03:03:58,810 [INFO] Found 1 chromosomes with overlapping regions
-2025-01-06 03:03:58,810 [INFO] Extending the regions by 500 bases
-2025-01-06 03:03:58,812 [INFO] Found 1 chromosomes with overlapping regions
-2025-01-06 03:03:58,942 [INFO] Zipped 2052 variants Counter({'base': 1132, 'comp': 920})
-2025-01-06 03:03:58,942 [INFO] 10 chunks of 2052 variants Counter({'__filtered': 2025, 'comp': 15, 'base': 12})
-2025-01-06 03:03:58,979 [INFO] Stats: {
+2025-01-06 19:48:57,901 [INFO] Including 11 bed regions
+2025-01-06 19:48:57,902 [INFO] Found 1 chromosomes with overlapping regions
+2025-01-06 19:48:57,902 [INFO] Extending the regions by 500 bases
+2025-01-06 19:48:57,903 [INFO] Found 1 chromosomes with overlapping regions
+2025-01-06 19:48:58,130 [INFO] Zipped 2052 variants Counter({'base': 1132, 'comp': 920})
+2025-01-06 19:48:58,131 [INFO] 10 chunks of 2052 variants Counter({'__filtered': 2025, 'comp': 15, 'base': 12})
+2025-01-06 19:48:58,167 [INFO] Stats: {
     "TP-base": 6,
     "TP-comp": 6,
     "FP": 4,
@@ -64,4 +64,4 @@
         }
     }
 }
-2025-01-06 03:03:58,979 [INFO] Finished bench
+2025-01-06 19:48:58,168 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz b/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_includebed/log.txt b/repo_utils/answer_key/bench/bench13_includebed/log.txt
@@ -1,6 +1,6 @@
-2025-01-06 03:03:57,421 [INFO] Truvari v5.0.0
-2025-01-06 03:03:57,421 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13_includebed/ --includebed repo_utils/test_files/beds/include.bed
-2025-01-06 03:03:57,422 [INFO] Params:
+2025-01-06 19:48:56,555 [INFO] Truvari v5.0.0
+2025-01-06 19:48:56,556 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13_includebed/ --includebed repo_utils/test_files/beds/include.bed
+2025-01-06 19:48:56,556 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz",
@@ -29,11 +29,11 @@
     "check_monref": true,
     "check_multi": true
 }
-2025-01-06 03:03:57,439 [INFO] Including 11 bed regions
-2025-01-06 03:03:57,440 [INFO] Found 1 chromosomes with overlapping regions
-2025-01-06 03:03:57,568 [INFO] Zipped 2032 variants Counter({'base': 1132, 'comp': 900})
-2025-01-06 03:03:57,568 [INFO] 9 chunks of 2032 variants Counter({'__filtered': 2009, 'base': 12, 'comp': 11})
-2025-01-06 03:03:57,606 [INFO] Stats: {
+2025-01-06 19:48:56,571 [INFO] Including 11 bed regions
+2025-01-06 19:48:56,572 [INFO] Found 1 chromosomes with overlapping regions
+2025-01-06 19:48:56,791 [INFO] Zipped 2032 variants Counter({'base': 1132, 'comp': 900})
+2025-01-06 19:48:56,792 [INFO] 9 chunks of 2032 variants Counter({'__filtered': 2009, 'base': 12, 'comp': 11})
+2025-01-06 19:48:56,828 [INFO] Stats: {
     "TP-base": 5,
     "TP-comp": 5,
     "FP": 4,
@@ -59,4 +59,4 @@
         }
     }
 }
-2025-01-06 03:03:57,607 [INFO] Finished bench
+2025-01-06 19:48:56,829 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/collapse/input1_collapsed.vcf b/repo_utils/answer_key/collapse/input1_collapsed.vcf
@@ -1177,9 +1177,9 @@ chr20	612157	.	T	G	60	.	QNAME=HG002-S9-H1-000001F;QSTART=591666;QSTRAND=+	GT:PL:
 chr20	612432	.	T	C	60	.	QNAME=HG002-S9-H1-000001F;QSTART=591941;QSTRAND=+	GT:PL:DP	1|1:9,5,8:19,42
 chr20	612664	.	T	C	60	.	QNAME=HG002-S9-H1-000001F;QSTART=592173;QSTRAND=+	GT:PL:DP	1|1:8,9,7:8,15
 chr20	612674	.	A	G	60	.	QNAME=HG002-S9-H1-000001F;QSTART=592183;QSTRAND=+	GT:PL:DP	1|0:8,3,2:5,28
+chr20	613783	.	T	<DEL>	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;END=613837;SVLEN=-54	GT:PL:DP	1/1:6,8,8:40,41
 chr20	613783	.	T	<DUP>	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DUP;END=613837;SVLEN=54	GT:PL:DP	1/1:6,8,8:40,41
-chr20	613783	.	TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG	CGTGCATGCTTAGCAGCAGTGGGAACCAAGGGACTTGAGCTGGACTCAGCACACA	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=INV;SVLEN=54	GT:PL:DP	1/1:6,8,8:40,41
-chr20	613783	.	TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG	T	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54	GT:PL:DP	1/1:6,8,8:40,41
+chr20	613783	.	T	<INV>	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=INV;END=613837;SVLEN=54	GT:PL:DP	1/1:6,8,8:40,41
 chr20	614408	.	C	T	60	.	QNAME=HG002-S9-H2-000001F;QSTART=568827;QSTRAND=+	GT:PL:DP	0|1:10,8,7:15,40
 chr20	614449	.	ATCTC	A	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593905;QSTRAND=+	GT:PL:DP	1|0:6,2,2:41,8
 chr20	614473	.	C	A	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593924;QSTRAND=+	GT:PL:DP	1|0:3,8,4:8,28

diff --git a/repo_utils/answer_key/collapse/input1_median_collapsed.vcf b/repo_utils/answer_key/collapse/input1_median_collapsed.vcf
@@ -1180,9 +1180,9 @@ chr20	612157	.	T	G	60	.	QNAME=HG002-S9-H1-000001F;QSTART=591666;QSTRAND=+	GT:PL:
 chr20	612432	.	T	C	60	.	QNAME=HG002-S9-H1-000001F;QSTART=591941;QSTRAND=+	GT:PL:DP	1|1:9,5,8:19,42
 chr20	612664	.	T	C	60	.	QNAME=HG002-S9-H1-000001F;QSTART=592173;QSTRAND=+	GT:PL:DP	1|1:8,9,7:8,15
 chr20	612674	.	A	G	60	.	QNAME=HG002-S9-H1-000001F;QSTART=592183;QSTRAND=+	GT:PL:DP	1|0:8,3,2:5,28
+chr20	613783	.	T	<DEL>	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;END=613837;SVLEN=-54	GT:PL:DP	1/1:6,8,8:40,41
 chr20	613783	.	T	<DUP>	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DUP;END=613837;SVLEN=54	GT:PL:DP	1/1:6,8,8:40,41
-chr20	613783	.	TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG	CGTGCATGCTTAGCAGCAGTGGGAACCAAGGGACTTGAGCTGGACTCAGCACACA	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=INV;SVLEN=54	GT:PL:DP	1/1:6,8,8:40,41
-chr20	613783	.	TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG	T	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54	GT:PL:DP	1/1:6,8,8:40,41
+chr20	613783	.	T	<INV>	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=INV;END=613837;SVLEN=54	GT:PL:DP	1/1:6,8,8:40,41
 chr20	614408	.	C	T	60	.	QNAME=HG002-S9-H2-000001F;QSTART=568827;QSTRAND=+	GT:PL:DP	0|1:10,8,7:15,40
 chr20	614449	.	ATCTC	A	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593905;QSTRAND=+	GT:PL:DP	1|0:6,2,2:41,8
 chr20	614473	.	C	A	60	.	QNAME=HG002-S9-H1-000001F;QSTART=593924;QSTRAND=+	GT:PL:DP	1|0:3,8,4:8,28

diff --git a/repo_utils/run_unittest.py b/repo_utils/run_unittest.py
@@ -3,7 +3,6 @@
 """
 import os
 import sys
-import pysam
 from collections import defaultdict
 from intervaltree import IntervalTree
 
@@ -22,10 +21,10 @@
 region_start = 10
 region_end = 20
 
-vcf = pysam.VariantFile(vcf_fn)
+vcf = truvari.VariantFile(vcf_fn)
 for entry in vcf:
     state = entry.info['include'] == 'in'
-    assert state == truvari.entry_within(entry, region_start, region_end), f"Bad Boundary {str(entry)}"
+    assert state == entry.within(region_start, region_end), f"Bad Boundary {str(entry)}"
 
 # removed
 #regions = truvari.RegionVCFIterator(vcf, includebed=bed_fn)
@@ -50,7 +49,7 @@
         data = line.strip().split()
         tree[data[0]].addi(int(data[1]), int(data[2]) + 1)
 
-vcf = pysam.VariantFile(vcf_fn)
+vcf = truvari.VariantFile(vcf_fn)
 for entry in truvari.region_filter(vcf, tree, True, False):
     assert entry.info['include'] == 'in', f"Bad in {str(entry)}"
 
@@ -59,23 +58,23 @@
     assert entry.info['include'] == 'out', f"Bad out {str(entry)}"
 
 
-vcf = pysam.VariantFile(vcf_fn)
+vcf = truvari.VariantFile(vcf_fn)
 for entry in truvari.region_filter_stream(vcf, tree, True, False):
     assert entry.info['include'] == 'in', f"Bad in {str(entry)}"
 
 vcf.reset()
 for entry in truvari.region_filter_stream(vcf, tree, False, False):
     assert entry.info['include'] == 'out', f"Bad out {str(entry)}"
 
-vcf = pysam.VariantFile(vcf_fn)
+vcf = truvari.VariantFile(vcf_fn)
 for entry in truvari.region_filter_fetch(vcf, tree, False):
     assert entry.info['include'] == 'in', f"Bad in {str(entry)}"
 
 
 """
 Filtering logic
 """
-vcf = pysam.VariantFile("repo_utils/test_files/variants/filter.vcf")
+vcf = truvari.VariantFile("repo_utils/test_files/variants/filter.vcf")
 matcher = truvari.Matcher()
 matcher.params.sizemin = 0
 matcher.params.sizefilt = 0

diff --git a/truvari/__init__.py b/truvari/__init__.py
@@ -1,20 +1,20 @@
 """
-
 Truvari - SV comparison and annotation toolkit
 
 See `help()` of specific functions / objects for details
 
-VariantRecord methods:
+Objects:
 
-:meth:`entry_is_present`
-:meth:`entry_reciprocal_overlap`
-:meth:`entry_same_variant_type`
-:meth:`entry_seq_similarity`
-:meth:`entry_size`
-:meth:`entry_size_similarity`
-:meth:`entry_to_hash`
-:meth:`entry_to_key`
-:meth:`entry_within`
+:class:`Bench`
+:class:`BenchOutput`
+:class:`GT`
+:class:`RegionVCFIterator`
+:class:`LogFileStderr`
+:class:`MatchResult`
+:class:`Matcher`
+:class:`StatsBox`
+:class:`SV`
+:class:`VariantRecord`
 
 Extra methods:
 
@@ -61,18 +61,6 @@
 :meth:`setup_logging`
 :meth:`vcf_to_df`
 
-Objects:
-
-:class:`Bench`
-:class:`BenchOutput`
-:class:`GT`
-:class:`RegionVCFIterator`
-:class:`LogFileStderr`
-:class:`MatchResult`
-:class:`Matcher`
-:class:`StatsBox`
-:class:`SV`
-
 Data:
 
 :data:`truvari.HEADERMAT`
@@ -101,16 +89,6 @@
 from truvari.comparisons import (
     best_seqsim,
     coords_within,
-    entry_is_present,
-    entry_reciprocal_overlap,
-    entry_same_variant_type,
-    entry_seq_similarity,
-    entry_size,
-    entry_size_similarity,
-    entry_to_hash,
-    entry_to_key,
-    entry_within_tree,
-    entry_within,
     overlap_percent,
     overlaps,
     reciprocal_overlap,
@@ -168,7 +146,8 @@
     vcf_ranges,
 )
 
-from truvari.variant_record import (
+from truvari.variants import (
+    VariantFile,
     VariantRecord,
 )
 

diff --git a/truvari/annotations/af_calc.py b/truvari/annotations/af_calc.py
@@ -138,7 +138,7 @@ def allele_freq_annos(entry, samples=None):
     Calculate allele annotations for a VCF Entry
 
     :param `entry`: Entry with samples to parse
-    :type `entry`: :class:`pysam.VariantRecord`
+    :type `entry`: :class:`truvari.VariantRecord`
     :param `samples`: Subset of samples from the entry over which to calculate annos
     :type `samples`: list of strings, optional
 
@@ -155,7 +155,7 @@ def allele_freq_annos(entry, samples=None):
     Example
         >>> import truvari
         >>> import pysam
-        >>> v = pysam.VariantFile('repo_utils/test_files/variants/multi.vcf.gz')
+        >>> v = truvari.VariantFile('repo_utils/test_files/variants/multi.vcf.gz')
         >>> truvari.allele_freq_annos(next(v))
         {'AF': 0.5, 'MAF': 0.5, 'ExcHet': 1.0, 'HWE': 1.0, 'MAC': 1, 'AC': [1, 1], 'AN': 2, 'N_HEMI': 0, 'N_HOMREF': 0, 'N_HET': 1, 'N_HOMALT': 0, 'N_MISS': 2}
     """

diff --git a/truvari/annotations/bpovl.py b/truvari/annotations/bpovl.py
@@ -4,7 +4,6 @@
 import logging
 import argparse
 
-import pysam
 import joblib
 import pandas as pd
 
@@ -62,7 +61,7 @@ def bpovl_main(cmdargs):
     Main method
     """
     args = parse_args(cmdargs)
-    in_vcf = pysam.VariantFile(args.input)
+    in_vcf = truvari.VariantFile(args.input)
     anno_tree, anno_cnt = truvari.build_anno_tree(args.anno, *args.anno_psets)
     logging.info("Loaded %d annotations", anno_cnt)
 
@@ -79,7 +78,7 @@ def _transform():
             if entry.size() < args.sizemin:
                 continue
 
-            key = truvari.entry_to_hash(entry)
+            key = entry.to_hash()
             for anno_idx in anno_tree[entry.chrom].at(start):
                 has_hit = True
                 yield [key, 'start_bnd', anno_idx.data]

diff --git a/truvari/annotations/chunks.py b/truvari/annotations/chunks.py
@@ -6,7 +6,6 @@
 """
 import sys
 import argparse
-import pysam
 
 import truvari
 from truvari.collapse import tree_size_chunker, tree_dist_chunker
@@ -41,15 +40,15 @@ def get_bounds(cnk):
     mend = 0
     for i in cnk:
         mstart = min(mstart, i.start)
-        mend = max(mend, i.stop)
+        mend = max(mend, i.end)
     return mstart, mend
 
 def chunks_main(args):
     """
     Main
     """
     args = parse_args(args)
-    v = pysam.VariantFile(args.input)
+    v = truvari.VariantFile(args.input)
     m = truvari.Matcher()
     m.params.pctseq = 0
     m.params.sizemin = args.sizemin